结球白菜结球期叶片的表达序列标签及基因表达分析
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摘要
结球白菜(Brassica rapa L．ssp．pekinensis)原产于我国，是我国北方地区的重要蔬菜之一。在长期的自然进化和人工选择的共同作用下，形成了以贮藏营养物质为功能器官的叶球。研究叶球的形成过程无疑对于提高大白菜的产量和品质有着重要的意义。目前有关结球机理的研究在国际范围内仍然处于起步阶段。为了从基因组水平了解结球期叶片的基因表达情况，实验室先前构建了结球白菜结球前期包心叶和球叶cDNA文库，通过对文库的进一步处理和分析，我们获得了以下主要结果：
利用λZipLox噬菌体侵染寄主菌DH10B，完成了cDNA文库中2967个阳性噬菌体克隆向质粒克隆的转变，并完成全部转化菌的质粒提取工作。随机挑选质粒进行序列测定，获得2802个较好的测序结果，其中1361个序列为自测，1441个序列由上海生工及鼎国生物技术公司测定。对影响测序反应的因素进行了探索，发现所用质粒模板的纯度和用量是影响测序成功与否的关键因素。
初步分析表明，插入片段长度小于150 bp或者全为polyA的序列共268个，没有任何插入片段的空载体序列有162个。去除以上两类序列后，共获得2372条可用于后续分析的有效EST序列，占全部序列的84.6％。全部片段总长度为1088467bp，平均每EST长度为459bp，高于同类物种EST研究报道的平均长度。
利用DNAStar软件中的SeqmanⅡ模块对2372条EST序列进行片段重叠群(contig)分析，共计获得1641个不同的片段重叠群，所有contig全长为782616bp，平均长度为477bp)。其中，1247个contig仅由一条EST组成(52.6％)，即singletons。结合blast比对结果，估算非冗余序列数目应在1499个左右，冗余序列约占EST总数的36.8％。
利用blastx程序，在蛋白质水平上与登录在NCBI非冗余蛋白质数据库(nr)中的序列进行比对后发现，1232个contig即1810条EST在数据库中可以找到同源物，占有效EST总数的76.3％。比对分值小于80及没有同源物的部分与est others数据库进行比对后，又有295个contig即432条EST可以找到同源EST，剩余的114个contig即131条EST仍然不能找到同源EST序列，这部分序列可认为是首次报道的EST序列。
物种来源上看，虽然功能已知的同源蛋白质中，来自拟南芥的占有绝大多数，但与est others数据库进行比对后，同源性最高的EST中只有51％来自拟南芥。说明结球白菜与拟南芥的基因表达模式存存较大差别。这部分相似性较低的序列，对于研究结球白菜独特的发育和代谢途径以及进行遗传作图具有特殊的意义。
同源物功能已知部分参照拟南芥研究中的方法，根据其同源蛋白的生物学作
用或生化功能分类，发现参与蛋白质合成的基因数量最多Q2．5％L 其次是参
与能量代谢O．7％L细胞防卫O．2o＼信号转导（7．lo）、细胞结构历．9O＼
初级代谢（6石％）、蛋白质修饰和加工储藏（6．4％）等途径的基因。与几种已发
表的双子叶植物叶片EST的功能分类研究比较后发现，在结球白菜结球叶中参
与蛋白质合成过程的蛋白质所占比例最大，而不像其它双于叶植物叶片EST研
究中以参与能量代谢过程的蛋白质占绝对优势。推测这种表达模式的差异可能与
白菜生长环境变化（如低温胁迫）及结球叶的旺盛生长有关。
通过提高反应混合物中引物和dNTP的浓度，对CDNA的全面扩增技术
oOlyAPCR）作了进一步的优化。杂交实验显示，白菜莲座期后期及结球期中
期叶片cDNA的扩增产物保持了起始mRNA的浓度比例关系，可以用于后续杂
交分析。利用载体两端通用引物，对所有挑选出的1438个CDNA克隆的质粒进
行了PCR扩增，按照基因功能模块分类，利用Bi小Rad公司的96孔Bi。－d帆点
膜工具先后共点制了 16对尼龙膜，并以标记的 cDNA扩增产物作为探针对所有
尼龙膜进行了杂交分析。
分析杂交结果，发现 152个杂交点在莲座期与结球中期叶片中表达量上有较
明显差异，其中94个为候选结球期上调表达类型，其余5 8个为结球期候选下调
表达类型。功能已知部分的候选基因中，表达水平上调部分主要集中于两类反应
途径：一是泛素蛋白“S蛋白酶体途径，二是低温胁迫抗逆反应途径。推测结球
期植株体内激素水平的改变和外界环境温度的下降可能是导致两类反应途径基
因表达水平改变的主要原因。Northern杂交验证候选基因中的类金属硫蛋白及一
功能未知基因，结果与点杂交一致，即前者在结球期呈现出上调表达模式，而后
者呈现出下调表达模式。同时还获得了类金属硫蛋白基因全长cDNA，Southern
杂交显示桔红心白菜基因组中该基因可能只有一个拷贝。
总之，本研究通过分析结球白菜结球前期叶片的表达序列标签（EST），构建
了虚拟的结球期叶片基因表达图谱，并采用大规模的点杂交实验研究了结球白菜
结球期叶片的基因表达情况。所获研究成果对于研究结球白菜的结球机理具有重
要的理论指导意义，同时在实践应用上，对于许多具有结球习性蔬菜的分于育种
也必将产生重要影响。
China is an origin center of Chinese cabbage {Brassica rapa L. ssp. pekinensis) which is one of the most important vegetables in Far East. Under the co-effects of natural evolution and artificial selection the leaf head serving as the nutrition deposited organ has been formed. Studying the mechanism of heading process is very important in practice, especially for the aim of increasing the yield and quality of Chinese cabbage. Unfortunately, the pace for studying the mechanism of heading formation is just at the begining so far. A A ZipLox mediated cDNA library using the leaves of Chinese cabbage at the early heading stage had been constructed, in order to explore the gene expression pattern of heading leaf from the genomics level. Our work was to achieve the designed aims by analyzing that library further. Several main results and conclusions were following:
After transfecting Escherichia coli DH10B with the A ZipLox cDNA library we finally got 2697 plasmid clones and exacted all the plasmid among them. Totally 2802 sequences with better results were acquired after sequencing with DNA sequencer (Beckman & Coulter CEQ8000 genetic analysis system) or with the help of two biological company Shenggong and Dingguo Co.. We also studied the factors influencing the sequencing reaction and found that high purity and appropriate amount of plasmid template were the vital factors for obtaining good sequencing results.
The sequencing results indicated that 268 clones had inserts shorter than 150bp or only polyA sequences and 162 clones had no cDNA inserts. The sequences of remaining 2372 clones, occupied 84.6 percent of all the sequencing results, were used for further analysis. Total length of all the usable sequences was 1088467 bp, and the average length per EST was 459 bp, which was longer than that of other researchers reported.
The SeqMan II module of DNAStar software was used for contig analysis of all the 2372 ESTs, and a total of 1641 different contigs were obtained. Total length of all the contigs' consensus sequence was 782616 bp, and each contig had 477 bases for average. Further analysis revealed that 1247 contigs belonged to singletons which included only one EST in one contig. Combined with the later blast align results we predicted that the real number of non-redundant sequences was around 1499, so the redundant sequence occupied about 36.8%.
After being compared with the non-redundant protein (nr) databases of NCBI using blastx program, 1232 contigs which included 1810 ESTs shared significant similarity with sequences registered in the database. For the sequences with lower score than 80 or even having no homologous in the nr database, biastn program was carried out for finding homological ESTs in the estothers database of NCBI. Searching results showed that 295 contigs which included 432 ESTs could find homologous, and the remaining 114 contigs accounting for 131 ESTs still could not find any homological ESTs. These new ESTs might be the sequences discovered firstly in the world.
By analyzing the homological proteins' sources of the organisms, it was found that majority of the functionally known protein came from Arabidopsis thaliana; however, at the nucleotide level, only 51% (1205/2372) of the total ESTs showing highest homology to ESTs coming from Arabidopsis thaliana. This result suggested that gene expression profiles of Chinese cabbage differ from that of Arabidopsis thaliana. Sequences with lower similarity to the Arabidopsis nucleotide could be specially used to study the unique developmental process and metabolic pathway in Chinese cabbage, and those sequences were also important for the genetic map drawing in the future.
For the ESTs whose homological protein had elucidatory functions, functional assignment was carried out based on the method used in the Arabidopsis thaliana genome sequencing initiative. The results revealed that ESTs of the genes involved in the process of protein synthesis had the highest proportion which took up 22.5 percent of all the analyzed ESTs, then in turn were the ESTs
利用λZipLox噬菌体侵染寄主菌DH10B，完成了cDNA文库中2967个阳性噬菌体克隆向质粒克隆的转变，并完成全部转化菌的质粒提取工作。随机挑选质粒进行序列测定，获得2802个较好的测序结果，其中1361个序列为自测，1441个序列由上海生工及鼎国生物技术公司测定。对影响测序反应的因素进行了探索，发现所用质粒模板的纯度和用量是影响测序成功与否的关键因素。
初步分析表明，插入片段长度小于150 bp或者全为polyA的序列共268个，没有任何插入片段的空载体序列有162个。去除以上两类序列后，共获得2372条可用于后续分析的有效EST序列，占全部序列的84.6％。全部片段总长度为1088467bp，平均每EST长度为459bp，高于同类物种EST研究报道的平均长度。
利用DNAStar软件中的SeqmanⅡ模块对2372条EST序列进行片段重叠群(contig)分析，共计获得1641个不同的片段重叠群，所有contig全长为782616bp，平均长度为477bp)。其中，1247个contig仅由一条EST组成(52.6％)，即singletons。结合blast比对结果，估算非冗余序列数目应在1499个左右，冗余序列约占EST总数的36.8％。
利用blastx程序，在蛋白质水平上与登录在NCBI非冗余蛋白质数据库(nr)中的序列进行比对后发现，1232个contig即1810条EST在数据库中可以找到同源物，占有效EST总数的76.3％。比对分值小于80及没有同源物的部分与est others数据库进行比对后，又有295个contig即432条EST可以找到同源EST，剩余的114个contig即131条EST仍然不能找到同源EST序列，这部分序列可认为是首次报道的EST序列。
物种来源上看，虽然功能已知的同源蛋白质中，来自拟南芥的占有绝大多数，但与est others数据库进行比对后，同源性最高的EST中只有51％来自拟南芥。说明结球白菜与拟南芥的基因表达模式存存较大差别。这部分相似性较低的序列，对于研究结球白菜独特的发育和代谢途径以及进行遗传作图具有特殊的意义。
同源物功能已知部分参照拟南芥研究中的方法，根据其同源蛋白的生物学作
用或生化功能分类，发现参与蛋白质合成的基因数量最多Q2．5％L 其次是参
与能量代谢O．7％L细胞防卫O．2o＼信号转导（7．lo）、细胞结构历．9O＼
初级代谢（6石％）、蛋白质修饰和加工储藏（6．4％）等途径的基因。与几种已发
表的双子叶植物叶片EST的功能分类研究比较后发现，在结球白菜结球叶中参
与蛋白质合成过程的蛋白质所占比例最大，而不像其它双于叶植物叶片EST研
究中以参与能量代谢过程的蛋白质占绝对优势。推测这种表达模式的差异可能与
白菜生长环境变化（如低温胁迫）及结球叶的旺盛生长有关。
通过提高反应混合物中引物和dNTP的浓度，对CDNA的全面扩增技术
oOlyAPCR）作了进一步的优化。杂交实验显示，白菜莲座期后期及结球期中
期叶片cDNA的扩增产物保持了起始mRNA的浓度比例关系，可以用于后续杂
交分析。利用载体两端通用引物，对所有挑选出的1438个CDNA克隆的质粒进
行了PCR扩增，按照基因功能模块分类，利用Bi小Rad公司的96孔Bi。－d帆点
膜工具先后共点制了 16对尼龙膜，并以标记的 cDNA扩增产物作为探针对所有
尼龙膜进行了杂交分析。
分析杂交结果，发现 152个杂交点在莲座期与结球中期叶片中表达量上有较
明显差异，其中94个为候选结球期上调表达类型，其余5 8个为结球期候选下调
表达类型。功能已知部分的候选基因中，表达水平上调部分主要集中于两类反应
途径：一是泛素蛋白“S蛋白酶体途径，二是低温胁迫抗逆反应途径。推测结球
期植株体内激素水平的改变和外界环境温度的下降可能是导致两类反应途径基
因表达水平改变的主要原因。Northern杂交验证候选基因中的类金属硫蛋白及一
功能未知基因，结果与点杂交一致，即前者在结球期呈现出上调表达模式，而后
者呈现出下调表达模式。同时还获得了类金属硫蛋白基因全长cDNA，Southern
杂交显示桔红心白菜基因组中该基因可能只有一个拷贝。
总之，本研究通过分析结球白菜结球前期叶片的表达序列标签（EST），构建
了虚拟的结球期叶片基因表达图谱，并采用大规模的点杂交实验研究了结球白菜
结球期叶片的基因表达情况。所获研究成果对于研究结球白菜的结球机理具有重
要的理论指导意义，同时在实践应用上，对于许多具有结球习性蔬菜的分于育种
也必将产生重要影响。
China is an origin center of Chinese cabbage {Brassica rapa L. ssp. pekinensis) which is one of the most important vegetables in Far East. Under the co-effects of natural evolution and artificial selection the leaf head serving as the nutrition deposited organ has been formed. Studying the mechanism of heading process is very important in practice, especially for the aim of increasing the yield and quality of Chinese cabbage. Unfortunately, the pace for studying the mechanism of heading formation is just at the begining so far. A A ZipLox mediated cDNA library using the leaves of Chinese cabbage at the early heading stage had been constructed, in order to explore the gene expression pattern of heading leaf from the genomics level. Our work was to achieve the designed aims by analyzing that library further. Several main results and conclusions were following:
After transfecting Escherichia coli DH10B with the A ZipLox cDNA library we finally got 2697 plasmid clones and exacted all the plasmid among them. Totally 2802 sequences with better results were acquired after sequencing with DNA sequencer (Beckman & Coulter CEQ8000 genetic analysis system) or with the help of two biological company Shenggong and Dingguo Co.. We also studied the factors influencing the sequencing reaction and found that high purity and appropriate amount of plasmid template were the vital factors for obtaining good sequencing results.
The sequencing results indicated that 268 clones had inserts shorter than 150bp or only polyA sequences and 162 clones had no cDNA inserts. The sequences of remaining 2372 clones, occupied 84.6 percent of all the sequencing results, were used for further analysis. Total length of all the usable sequences was 1088467 bp, and the average length per EST was 459 bp, which was longer than that of other researchers reported.
The SeqMan II module of DNAStar software was used for contig analysis of all the 2372 ESTs, and a total of 1641 different contigs were obtained. Total length of all the contigs' consensus sequence was 782616 bp, and each contig had 477 bases for average. Further analysis revealed that 1247 contigs belonged to singletons which included only one EST in one contig. Combined with the later blast align results we predicted that the real number of non-redundant sequences was around 1499, so the redundant sequence occupied about 36.8%.
After being compared with the non-redundant protein (nr) databases of NCBI using blastx program, 1232 contigs which included 1810 ESTs shared significant similarity with sequences registered in the database. For the sequences with lower score than 80 or even having no homologous in the nr database, biastn program was carried out for finding homological ESTs in the estothers database of NCBI. Searching results showed that 295 contigs which included 432 ESTs could find homologous, and the remaining 114 contigs accounting for 131 ESTs still could not find any homological ESTs. These new ESTs might be the sequences discovered firstly in the world.
By analyzing the homological proteins' sources of the organisms, it was found that majority of the functionally known protein came from Arabidopsis thaliana; however, at the nucleotide level, only 51% (1205/2372) of the total ESTs showing highest homology to ESTs coming from Arabidopsis thaliana. This result suggested that gene expression profiles of Chinese cabbage differ from that of Arabidopsis thaliana. Sequences with lower similarity to the Arabidopsis nucleotide could be specially used to study the unique developmental process and metabolic pathway in Chinese cabbage, and those sequences were also important for the genetic map drawing in the future.
For the ESTs whose homological protein had elucidatory functions, functional assignment was carried out based on the method used in the Arabidopsis thaliana genome sequencing initiative. The results revealed that ESTs of the genes involved in the process of protein synthesis had the highest proportion which took up 22.5 percent of all the analyzed ESTs, then in turn were the ESTs
引文
1．李家文(1984)《中国大白菜》．北京：农业出版社．71-75
2．郭晶心，周乃元，马荣才，曹鸣庆(2003)利用mRNA差别显示技术研究大白菜结球过程中的基因表达 农业生物技术学报 11，456-460
3．严继勇 (2004)BcpLH反义基因在大白菜中的转化及其功能的研究 浙江大学博士学位论文
4．杨素欣，冯献忠，刘平林，何玉科．(2000)甘蓝中BcpLH同源基因的克隆及其表达分析．植物生理学报 26，363-368
5．余旭红，彭洁松，冯献忠，郑志仁，杨素欣，唐向荣，沈瑞娟，刘平林，何玉科．(2000)大白菜包叶特异基因的克隆及其结构特征和表达方式．中国科学(C辑)30，475-482
6．甄志成，姚志建．(2001)毛细管阵列电泳与规模化DNA测序．色谱19，361-364
7. Ablett, E., Seaton, G., Scott, K. and Shelton, D. (2000) Analysis of grape ESTs: global gene expression patterns in leaf and berry. Plant Sci. 159,87-95
8. Adams M.D., Kelley J.K., Gocayne J.D., Dubnick M., Polymeropoulos M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., Kerlavage A.R., McCombie W.R. and Venter J.C. (1991)Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252,1651-1656
9. Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman DJ. (1990) Basic local alignment search tool. J Mol. Biol. 215,403-410
10. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25,3389-3402
11. Allona I., Quinn M., Shoop E., Swope K., Cyr S.S., Carlis J., Riedl J., Retzel E., Campbell M.M., Sederoff R. and Whetten R.W. (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc. Natl. Acad. Sci. USA 95,9693-9698
12. Anderson, I. and Brass, A. (1998) Searching DNA databases for similarities to DNA sequences: when is a match significant? Bioinformatics 14,349-356.
13. Audic, S. and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res. 7,986-995
14. Babula D,, Kaczmarek M., Barakat A., Delseny M., Quiros C.F. and Sadowski J. (2003) Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map. Mol. Gen. Genomics 268,656-665
15. Baker, S.S., Wilhelm, K.S., and Thomashow, M.F. (1994) The 5'-region of Arabidopsis thaliana COR15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol. Biol. 24,701-713
16. Bailey, P.C., Martin, C., Toledo-Ortiz G., Quail, P.H., Huq, E., Heim, M.A., Jakoby, M. and Weisshaar B. (2003) Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana. Plant Cell 15, 2497-2501
17. Barakat, A., Szick-Miranda, K., Chang, I. F. and Guyot, R. (2001) The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol. 127,398-415
18. Baugh L. R., Hill A. A., Brown E. L. and Hunter C.P. (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29,e29
19. Bell C.J., Dixon R.A., Farmer A.D., Flores R., Inman J., Gonzales R.A., Harrison M.J., Paiva N.L., Scott A.D., Weller J.W. and May G.D, (2001) The Medicago Genome Initiative: a model legume database. Nucleic Acids Res. 29(1), 114-117
20. Belyavsky A., Vinogradova T. and Rajewsky K. (1989) PCR-based cDNA library construction: general cDNA libraries at the level of a few cells. Nucleic Acids Res. 17,2919-2932
21. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. and Wheeler D.L. (2003) GeneBank. Nucleic Acids Res. 31, 23-27
22. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. and Wheeler D.L. (2004) GeneBank: update. Nucleic Acids Res. 32, D23-D26
23. Bevan, M., Bancroft, I., Bent, E. and Love, K. (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391,485-488
24. Brady, G.., Barbara, M. and Iscove, N.N. (1990) Representative in vitro cDNA amplication from individual hemopoietic cells and elonies. Methods Mol. Cell. Biol. 2, 17-15.
25. Brady, G. and Iscove, N.N. (1993) Construction of cDNA libraries from single cells. Yeast 225, 611-623.
26. Brandle J.E., Richman A., Swanson A.K. and Chapman B.P. (2002) Leaf ESTs from Stevia rebaudiana: a resource for gene discovery in diterpene synthesis. Plant Mol. Biol. 50,613-622
27. Bryant Z., Subrahmanyan L. and Tworoger M. (1999) Charatedzation of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proc. Natl. Acad Sci. USA 96,5559-5564
28. Broglie, K., Chet, I., Hollyday, M., Cressrnan, R., Biddle, P., Knowlton, S., Mauvais, C.J., and Broglie, R. (1991). Transgenic plants with enhanced resistance to the fungal pathogen Rhizoctonia solani. Science 254, 1194-1197.
29. Buchanan-Wollaston V. (1994) Isolation of cDNA clones for genes that are expressed during leaf senescence in Brassica napus: identification of a gene encoding a senescence-specific metallothionein-like protein. Plant Physiol. 105, 839--846.
30. Buetow K.H., Edmonson M.N. and Cassidy A.B. (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet. 21,323-325
31. Burr B. (2002) Mapping and sequencing the rice genome. Plant Cell 14, 521-523
32. Callis, J. and Vierstra, R.D. (2000) Protein degradation in signaling. Cure. Opin. Plant Biol. 3,381-386
33. Castro, N.C., Gotuzzo, E., Rodriguez, M., and Guerra, H. (2000) Clinical Application of a Dot Blot Test for Diagnosis of Enteric Fever Due to Salmonella enterica Serovar Typhi in Patients with Typhoid Fever from Colombia and Peru. Clinical and Diagnostic Laboratory Immunology 7, 312-313
34. Cato S.A., Gardner R.C., Kent J. and Richardson T.E. (2001) A rapid PCR-based method for genetically mapping ESTs. Theor Appl. Genet. 102,296-306
35. Chenchik, A., Diachenko, L., Moqadam, F., Tarabykin, V., Lukyanov, S. and Siebert, P.D. (1996) Full-Length cDNA Cloning and Determination of mRNA 5' and 3' Ends by Amplification of Adaptor-Ligated cDNA. BioTechniques 21,526-534
36. Choi, D., Kim, H.M., Yun, H.K., Park, J.A., Kim, W.T. and Bok, S.H. (1996) Molecular cloning of a metallonthionein-like gene from Nicotiana glutinosa L. and its induction by wounding and tobacco mosaic virus infection. Plant Physiol. 112,353-359
37. Chou H.H., Holmes M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17,1093-1104
38. Colling, D.B., Kragh, K.M., Mikkelsen, J.D., Nielsen, K.K., Rasmussen, U., and Vad, K. (1993). Plant chitnases. Plant J. 3,31-40
39. Connors B.J., Maynard C.A. and Powell W.A. (2001) Expressed sequence tags from stem tissue of the American chestnut, Castanea dentate. Biotech. Lett. 23,1407-1411
40. Cooke R., Raynal M., Laudie M. and Delseny M. (1997) Identification of members of gene families in Arabidopsis thalana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J. 11,1127-1140
41. Covitz P. A., Smith L.S. and Long S.R. (1998) Expressed sequence tags from a root-hair-enriched Medicago truncatula cDNA library. Plant Physiol. 117,1325-1332
42. del Pozo J.C., Dharmasiri, S., Hellmann, H., Walker, L., Gray, W.M., and Estelle, M. (2002) AXR1-ECR1-dependent conjugation of RUB1 to the Arabidopsis cullin AtCull is required for Auxin response. Plant Cell 14,421-433
43. Delseny M., Cooke R., Raynal M. and Grellet F. (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett. 403,221-224
44. Dixon A.K., Richardson P. J., Lee K., Carter N.P. and Freeman T. C. (1998) Expresion profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Res. 26,4426-4431
45. Duggan D.J., Bittner M., Chen Y.D., Meltzer P. and Trent J.M.(1999) Expression profiling using cDNA microarrays. Nature Gent. 21,10-14.
46. Dunn M. A., Hughes M. A., Zhang L., Pearce R.S., Quigley A.S. and Jack P. L. (1991) Nucleotide sequence and molecular analysis of the low temperature induced cereal gene, BLT4. Mol. Gen. Genet. 229,389-394
47. Eckardt N.A. (2000) Sequencing the rice genome. Plant Cell 12, 2011-2017
48. Epple P., Aple K. and Bohlmann H. (1997) ESTs reveal a multigene family for plant defensisns in Arabidopsis thaliana. FEBS Lett. 400, 168-172
49. Ewing B., Hillier L., Wendl M.C. and Green P. (1998) Base-calling of automated sequencer traces using phred. Accuracy assessment. Genome Res. 8,175-185
50. Ewing R.M., Kahla A.B., Poirot O., Lopez F., Audic S. and Claverie J.M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene espression. Genome Res. 9,950-959
51. Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y., Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S, Tang Y., Weng Q., Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T., Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R., Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G., Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C., Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J., Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J., Li J., Hong G., Xue Y. and Han B. (2002) Sequence and analysis of rice chromosome 4. Nature 420,316-320
52. Fowler, S. and Thomashow, M.F. (2002) Arabidopsis transcriptome profiling indicates that multiple regulatiory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14,1675-1690
53. Gang D.R., Wangg J., Dudareva N., Nam K.H., Simon J.E., Lewinsohn E. and Pichersky E. (2001) An investigation of the storage and biosynesis of phenylpropenes in sweet basil. Plant Physiol. 125,539-555
54. Galat, A. and Metcalfe, S. (1995) Peptidyl prolyl cis-trans isomerases. Prog. Biophys. Mol. Biol. 63, 67-118
55. Genund C., Ramu C., Altenberg-Greulich B. and Gibson T.J. (2001) Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with
eukaryotic gene-sized queries. Nucleic Acids Res. 29,1272-1277
56. Craham, L.S., and Sticklen, M.B. (1994). Plant chitinases. Can. J. Bot. 72, 1057-1083.
57. Gray, W.M., del Pozo, J.C., Walker, L., Hobbie, L., Risseeuw, E., Banks, T., Crosby, W. L., Yang, M., and Estelle, M. (1999) Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. Genes Dev. 13,1675-1691
58. Grivet L., Glaszmann J.C., Vincentz M., da Silva E and Arruda P. (2002) ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes. Theor. Appl. Genet. 106, 190-197
59. Gyorgyey J., Vaubert D., Jimenez-Zurdo J.I., Charon C., Troussard L., Kondorosi A. and Kondorosi E. (2000) Analysis ofMedicago truncatula nodule expressed sequence tags. Mol. Plant-Microbe Inter. 13,62-71
60. Hatey F., Tosser-Klopp G., Clouscard-Martinato C., Mulsant P. and Gasser F. (1998) Expressed sequence tags for genes: a review. Genet Sel. Evol. 30,521-541
61. Hays D.B. and Skinner D.Z. (2001) Development of an expressed sequence tag (EST) library for Medicago sativa. Plant Sci. 161,517-526
62. Hellmann, H. and Estelle, M. (2002) Plant development: regulation by protein degradation. Science 297,793-797
63. He, Y.K., Xue, W.X., Sun, Y.D., Yu, X.H. and Liu, P.L. (2000) Leafy head formation of the progenies of transgenic plants of Chinese cabbage with exogenous auxin genes. Cell Res. 10,151-60
64. Hofte H., Desprez T., Amselem J., Chiapello H., Rouze P., Caboche M., Moisan A., Jourjon M.F., Charpenteau J.L., Berthomieu P., Guerrier D., Giraudat J., Quigley F., Yu D.Y., Mache R., Raynal M., Cooke R., Grellet F., Delseny M., Parmentier Y., de Marcillac G., Gigot C., Fleck J., Philipps G., Axelos M., Bardet C., Tremousayue D. and Lescure B. (1993) An inventory of 1152 expressed sequence tags obtained by partial Sequencing of cDNAs from Arabidopsis thaliana. Plant J. 4,1051-1061
65. Hsiung, W.G., Chang, H.C., Pellequer, J.L., La Valle, R., Lanker, S., and Wittenberg, C. (2001) F-box protein Grrl interacts with phosphorylated targets via the cationic surface of its leucine-rich repeat. Mol. Cell. Biol. 19, 989-1001
66. Huang X.Q. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9,868-877
67. Iqbal, M.J., Yaegashi, S., Njiti, V.N. and Absan, R. (2002) Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f.sp. glycines. Mol. Genct. Genomics 268,407-417
68. Iscove, N.N., Barbara, M., Gu, M., Gibson, M., Modi, C. and Winegarden, N.(2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 20, 940-943.
69. Ito H, Kato T. (1957) Studies on the head formation of Chinese cabbage: histological and physiological studies of head formation. J. Jpn. Soc. Hortic. Sci. 26,154-204
70. Jach, Q, Grnhardt, B., Mundy, J., Logemann, J., Pinsdorf, E., Leah, R., Schell, J., and Maas, C. (1995) Enhanced quantitative resistance against fungal disease by combinatorial expression of different barley antifungal proteins in transgenic tobacco. Plant J. 8, 97-109.
71. Jain, A.K.(2001) Identification of drought-responsive transcripts in peanut (Arachis hypogaea L.) Elect. J. Biotechnol. 4,59-67
72. Jiang, C., Iu, B., and Singh, J. (1996) Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol. Biol. 30,679-684
73. Jones D.T. and Swindells M.B. (2002) Getting the most from PSI-BLAST. Trends Biochem. Sci. 27, 161-164
74. Joshi, C.P. (1987) An inspection of the domain between putative TATA box and translation start site in 79 plants. Nucleic Acids Res. 15,6643-6653
75. Jung, S.H., Lee, J.Y., and Lee, D.H. (2003) Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol.Biol. 52,553-567
76. Kanaya, E., Nakajima, N., Morikawa, K., Okada, K. and Shimura, Y. (1999) Characterization of the transcriptional activator CBF1 from Arabidopsis thaliana. J. Biol. Chem. 274,16068-16076
77. Kenzelmann M., Klaren R., Hergenhahn M., Bonrouhi M., Grone H.J., Schmid W. and Schutz G. (2004) High-accuracy amplification of nanogrm total RNA amounts for gene profiling. Genomics 83,550-558
78. Kepinski, S. and Leyser, O. (2002) Ubiquitination and auxin signaling: A degrading story. Plant Cell S81-S95
79. Kim, G.T. and Tsukaya, H. (2002) Regulation of the biosynthesis of plant hormones by cytochrome P450s. J.Plant Res. 115,169-177
80. Kitashiba,H., Iwai, T., Toriyama, K., Watanabe, M. and Hinata, K. (1996) Identification of genes expressed in the shoot apex of Brassica campestris during floral transition. Sex Plant Reprod 9,186-188
81. Knight, H., Trewavas A.J. and Knight M.R. (1996) Cold Calcium Signaling in Arabidopsis Involves Two Cellular Pools and a Change in Calcium Signature after Acclimation. Plant Cell 8,489-503
82. Kota R, Varshney RK, Thiel T, Dehmer KJ and Graner A. (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgate L.). Hereditas 135,145-151
83. Kreps, J. A., Wu, Y., Chang, H. S. and Zhu, T. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130,2129-2141
84. Krishna, P., Sacco, M., Cherutti, J.F. and Hill, S. (1995) Cold-Induced Accumulation of hsp90 Transcripts in Brassica napus. Plant Physiol. 107,915-923
85. Kwak J.M., Kim S.A., Hong S.W. and Nam H.G. (1997) Evaluation of 515 expressed sequence tags obtained from guard cells of Brassica campestris. Planta 202,9-17
86. Lan T.H., DelMonte T.A., Reisehmann K.P., Hyman J., Kowalski S.P., McFerson J., Kresovich S. and Paterson A.H. (2000) An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res. 10,776-788
87. Lee, J.Y. and Lee D.H. (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol. 132,517-529
88. Liang F., Holt I., Pertea G., Karamycheva S., Saizberg S.L. and Quackenbush J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28,3657-3665
89. Liang P. and Pardee A.B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257,967-971
90. Lim, C.O., Kim, H.Y., Kim, M.G., Lee, S.I., Chung, W.S., Park, S.H., Hwang, I. and Cho, M.J. (1996) Expressed sequence tags of Chinese cabbage flower bud cDNA. Plant Physiol. 111,577-588
91. Lim, J.Y.., Shim, C.S., Chung, E.J., Kim, J.S., Kim, H.U., Oh, S.J., Choi, W.B., Ryou, C.S., Kim, J.B., Kwon, M.S., Chung, T.Y., Song, S.I., Kim, J.K., Nahm, B.H., Hwang, Y.S., Eun, M.Y., Lee, J.S., Cheong, J.J. and Choi, Y.D. (2000) Analysis of expressed
sequence tags from Brassica rapa L.ssp.pekinensis. Mol.Cells 10,399-404
92. Lin, X.Y., Kaul, S., Rounsley, S., Shea, T.E, Benito, M.I., Town, C.D., Fujii, C.Y., Mason, T., Bowman, C.L., Barnstead, M., Feldblyum, T.V., Buell, C.R., Ketchum, K.A., Lee, J., Ronning, C.M., Koo, H.L., Moffat, K.S., Cronin, L.A., Shen, M., Pai, G., Aken, S.V., Umayam, L., Tallon, L.J., Gill, J.E., Adams, M.D., Carrera, A.J., Creasy, T.H., Goodman, H.M., Somerville, C.R., Copenhaver, G. P., Preuss, D., Nierman, W.C., White, O., Eisen, J.A., Salzberg, S.L., Fraser, C.M. and Venter, J.C.. (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768
93. Liu J.Y., Hara C., Umeda M., Zhao Y., Okita W. and Uchimiya H. (1995) Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L.): evaluation of expressed sequence tags, and expression levels of mRNAs. Plant Mol. Biol. 29,685-689
94. Lonsdale D., Crowe M., Arnold B. and Arnold B.C. (2001) Mendel-GFDb and Mendel-ESTs: databases of plant gene families and ESTs annotated with gent family numbers and gene family names. Nucleic Acids Res. 29,120-122
95. Luo M., Kong X.Y., Jiang T., Jia C., Zhou R.H., Jia J.Z. (2002) Analysis of resistance to powdery mildew in wheat based on expressed sequence tags (EST) technique. Acta Botanica Sinica 44,567-572
96. Martin K.J. and Pardee A.B. (2000) Identifying expressed genes. Proc. Natl. Acad. Sci. USA 97,3789-3791
97. Meinke D.W., Cherry J.M., Dean C.D., Rounsley S. and Koornneef M. (1998) Arabidopsis thaliana: a model plant for genome analysis. Science 282,662-682
98. Medina, F.J., Cerdido, A., and de Caxcer, G. (2000) The functional organization of the nucleolus in proliferating plant cells. Eur. J. Histochem. 44,117-131
99. Michalek W, Weschke W, Pleissner KP and Graner A. (2002) EST analysis in barley defines a unigene set comprising 4000 genes. Theor. Appl. Genet. 104,97-103
100. Murphy, A. and Taiz, L. (1995) Compadsion of metallothionein gene expression and nonprotein thiols in ten Arabidopsis ecorypes. Plant Physiol. 109,945-954
101. Neven, L.G., Haskell, D.W., Guy, C.L., Denslow, N., Klein, P.A., Green, L.G. and Silverman, A. (1992) Association of 70-kilodalton heat-shock cognate proteins with acclimation to cold. Plant Physiol. 99,1362-1369
102. Newman, T., Bruijn, F.J.D., Green, P., Keegstra, K, Kende, H., McIntosh, L., OhIrogge, J., Raikhel, N.,, Somerville, S., Thomashow, M., Retzel, E. and Somerville, C. (1994) Genes galore: A summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106,1241-1255
103. Nikaldo I., Asamizu E., Nakajima M., Nakamura Y., Saga N. and Tabata S. (2000) Generation of 10154 expressed sequence tags from a leafy gametophyte of a marine Red Alga, Porphyra yezoensis. DNA Res. 7,223-227
104. Ohlrogge J. and Benning C. (2000) Unraveling plant metabolism by EST analysis. Curr. Opin. Plant Biol. 3,224-228
105. Olson M., Hood L., Cantor C. and Botstein D. (1989) A common language for physical mapping of the human genome. Science 245,1434-1435
106. Oweas-Grillo, J.K., Hofman, K., Hutchison, K.A., Yem, A.W., Deibel, M.R., Handschumacher, J.R.E. and Pratt, W.B. (1995) The cyclosporine A-binding immunophilin Cyp-40 and the FK506-binding immunophilin HSP56 bind to a common site on HSP90 and exist in independent cytosolie heterocomplexes with the untransformed glucocorticoid receptor. J Biol Chem 270, 20479-20484
107. Puskas L.G., Zvara A., Hackler L., Jr and Van Hummelen P. (2002) RNA
amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32,1330-1340
108. Petalidis L., Bhattacharyya S., Morris G.A., Collins V.P., Freeman T.C. and Lyons P.A. (2003) Global amplification of mRNA by template-swiching PCR: linearity and applification to microarray analysis. Nucleic Acids Res. 31, e142
109. Pickart, C.M. (2001) Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503-533
110. Picoult-Newberg L., Ideker T.E., Pohl M.G., Taylor S.L., Donaldson M.A., Nickerson D.A.and Boyce-Jacino M. (1999) Mining SNPs from EST databases. Genome Res. 9,167-174
111. Provart, N.J., Gil, P., Chen, W. and Han, B. (2003) Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures. Plant Physiol. 132,893-906
112. Qin L., Prins P., Jones J.T., Popeijus H., Smant G., Bakker J. and Helder J. (2001) GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP. Nucleic Acids Res. 29,1616-1622
113. Quackenbush J., Cho J., Lee D., Liang F., Holt I., Karamycheva S., Parvizi B., Pertea G., Sultana R. and White J. (2001) The TIGR Gene Indices: analysis of gene transcript sequences in higly sampled eukaryotic species. Nucleic Acids Res. 29,159-164
114. Reichler, S.A., Balk, J., Brown, M. E., Woodruff, K. (2001) Light differentially regulates cell division and the mRNA abundance of pea nucleolin during de-etiolation. Plant Physiol. 125,339-350
115. Ronning C.M., Stegalkina S.S., Ascenzi R.A., Bougri O., Hart A.L., Utterbach T.R., Vanaken S.E., Riedmuller S.B., White J.A., Cho J., Pertea G.M., Lee Y.D., Karamycheva S., Sultana R., Tsai J., Quackenbush J., Griffiths H.M., Restrepo S., Smart C.D., Fry W.E., der Hoeven R.V., Tanksley S., Zhang P.F., Jin H.L., Yamamoto M.L., Baker B.J. and Buell CR. (2003) Comparative analyses of Potato expressed sequence tag libraries. Plant Physiol. 131,419-429
116. Ruan Y.J., Gilmore J. and Conner T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15,821-833
117. Saghizadeh M., Brown D. J., Tajbakhsh J., Chen Z., Kenney C., Farber D.B. and Nelson S.F. (2003) Evaluation of techniques using amplified nucleic acid probes for gene expression profiling. Biomol. Eng. 20,97-106
118. Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Blacker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech E, De S., V., Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Querier F., Schafer M., Muller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Lohnert T.H., Nordsiek G, Reichelt J., Scharfe M., Schon O., Bargues M., Terol J., Climent J., Navarro E, Collado C., Perez-Perez A., Ottenwalder B., Duehemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.P., Cottet A., Casacuberta E., Monfort A., Argiriou A., flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., School H., Rudd S., Zaccaria P., Mewes H.., Mayer K.F., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G,
Militscher J., Sellers E, Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M. and Tabata S. (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408, 820-822
119. Sasaki T., Song J.Y., Ban Y.K., Matsui E., Fang F., Higo H., Nagasaki H., Hori M., Miya M., Kayano E.M., Takiguchi T., Takasuga A., Niki T., Ishimaru K., Ikeda H., Yamarnoto Y., Mukai Y., Ohta I., Miyadera N., Havukkala I. and Minobe Y. (1994) Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus eDNA library. Plant J. 6,615-624
120. Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H., Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M., Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A, Kamiya K., Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K., Waki K, Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.I., Eun M.Y., Yano M., Jiang J. and Gojobori T. (2002) The genome sequence and structure of rice chromosome 1. Nature 420, 312-316
121. Scott K.D., Eggler P., Seaton G, Rossetto M., Ablett E.M., Lee L.S. and Henry R.J. (2000) Analysis of SSRs derived from grape ESTs. Theor. Appl. Genet. 100,723-726
122. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K. (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13,61-72
123. Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Caminci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A. and Shinozaki K. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296,141-145
124. Seth D., Correll M.D., McGuinness P.H. Leo M.A., Lieber C.S., MeCaughan G.W. and Haber P.S. (2003) SMART amplification maintains representation of relative gene expression: quantitative validation by real time PCR and application to studies of alcoholic liver disease in primates. J. Biochem. Biophys. Methods 55,53-66
125. Shen, B., Carneiro, N., Torres-Jerez, I., Stevenson, B. (1994) Partial sequencing and mapping of clones from two maize cDNA libraries. Plant Mol.Biol. 26,1085-1101
126. Smith L., Underhill P., Pritchard C., Tymowska-Latanne Z., Abdul-Hussein S., Hilton H., Winchester L., Williams D., Freeman T., Webb S. and Greenfield A. (2003) Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res. 31,e9
127. Sota A., Allona, I., Collada, C., Guevara, M.A., Casado, R., Cerezo, E.R., Aragoncillo, C. and Gomez L. (1999) Heterologous expression of a plant small heat-shock protein enhances Escherichia coli viabiligy under heat and cold stress. Plant Physiol. 120,521-528
128. Sutton, G, White, O., Adams, M., and Kerlavage, A. (1995) TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Science & Technology 1,9-19
129. Sterky F., Regan S., Karlsson J., Hertzberg M., Rohde A., Holmberg A., Amini B., Bhalerao R., Larsson M., Villarroel R., Montagu M.V., Sandberg G., Olsson O., Teeri T.T., Boerjan W., Gustafsson P., Uhlen M., Sundberg B. and Lundcrbcrg J. (1998) Gone discovery in the wood-forming tissue of poplar: analysis of 5692 expressed sequence tags. Proc. Natl. Acad Sci. USA 95,13330-13335
130. Stockinger, E.J., Gilmour, S.J., and Thomashow, M.F. (1997) Arabidopsis thaliana CBF1 enoodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. USA 94,1035-1040
131. Stump, M.D., Cherry J.L. and Weiss R.B. (1999) The use of modified palmers to eliminate cycle sequencing artifacts. Nucleic Acids Res. 27,4642-4648
132. Tabaei-Aghdaei, S.R., Pearce, R.S., and Harrison, P. (2003) Sugars regulate cold-induced gene expression and freezing-tolerance in barley cell cultures. J. Exp.Bot. 54,1565-1575
133. Thtiharju, S., Sangwan V., Monroy, A.F., Dhindsa, R.S. and Borg M. (1997) The induction of kin genes in cold-acclimating Arabidopsis thaliana. Evidence of a role for calcium. Planta 203,442-447
134. Thiel T., Michalek W., Varshney K. and Graner A. (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgate L.). Theor. Appl. Genet. 106,411-422
135. Thomas, D.J., Thomas, J.B., Prier, S.D., Nasso, N. E. and Herbert S. K. (1999) Iron Superoxide Dismutase Protects against Chilling Damage in the Cyanobacterium Synechococcus species PCC7942. Plant Physiol. 120,275-282
136. Trevio M.B. and Connell M.A. (1998) Three Drought-Responsive Members of the Nonspecific Lipid-Transfer Protein Gene Family in Lycopersicon pennellii Show Different Developmental Patterns of Expression. Plant Physiol. 116, 1461-1468
137. Trumper L.H., Brady G. and Bagg A. (1993) Single-cell analysis of Hodgkin and Reed-Sternberg cells: molecular heterogeneity of gene expression and p53 mutations. Blood 81,3097-3115
138. Trumper L.H., Brady G., Vicini S., Cossman J. and Mak T.W. (1992) Gene expression in single Reed-Sternberg cells of Hodgkin's disease: results from PCR-generated single-cell cDNA libraries. Ann. Oncol. 3 (suppl 4),25-26
139. Tsang, W.T., Bowler, C., Camp, H. D., Villarroel, W.V.R., Genetello, C., Montagu, M.V. and Inze D. (1991) Differential Regulation of Superoxide Dismutases in Plants Exposed to Environmental Stress. Plant Cell 3,783-792
140. Tuteja, R. and Tuteja, N. (1998) Nucleolin: a multifunctional major nuclcolar phosphoprotein. Crit. Rev.Biochem.Mol.Biol. 33,407-436
141. Velculescu V.E., Zhang L., Vogelstein B. and Kinzler K.W. (1995) Serial analysis of gene expression. Science 270, 484-487
142. Vierstra, R.D. (2003) The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends in Plant Sci. 8,135-142
143. Voiblet, C., Duplessis, S., Encelot, N., and Martin, F. (2001) Identification of symbiosis-regulated genes in Eucalyptus globules-Pisolithus tinctorius ectomycorrhiza by differential hybridization of arrayed cDNAs. Plant J. 25,181-191
144. Wang E., Miller, L. D., Ohnmaeht, G A., Liu E. T. and Marincola F. M. (2000) High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18,457-459
145. Wang W., Wyekof J.B., Wang Y., Bottinger E.P., Segall J.E. and Condeelis J.S. (2003) Gene expression analysis on small numbers of invasive cells collected by chemotaxis from primary mammary tumors of the mouse. BMC Biotechnol. 3,13-24
146. Wheeler D.L., Church D.M., Federhen S., Lash A.E., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E., Tatusova T.A. and Wagner L. (2003) Database resources of the national center for biotechnology. Nucleic Acids Res. 31,28-33
147. White J.A., Todd J., Newman T., Foeks N., Girke T., De Harduya O.M., Jaworski J.G., Ohlrogge J.B. and Benning C. (2000) A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol. 124,1582-1594
148. Wirtz K.W.A. and Cradella T.W.J. (1990) Properties and modes of action of specific and nonspecifie phospholipid transfer proteins. Experientia 46, 592-599
149. Wortey, C.K., Zenser, N., Ramos, J., Rouse, D., Leyser, O., Theologis, A., and Callis, J. (2000) Degradation of Aux/IAA proteins is essential for normal auxin signaling. Plant J. 21,553-562
150. Xue, G. P. (2002) An AP2 domain transcription factor HvCBF1 activates expression of cold-res-ponsive genes in barley through interaction with a (G/a)(C/t)CGAC motif. Biochim.Biophys.Acta 1577,63-72
151. Xue, G..P. and Loveridge, C.W. (2004) HvDRF1 is involved in abseisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element. Plant J. 37,326-339
152. Yamamoto K and Sasaki T. (1997) Large-scale EST sequencing in rice. Plant Mol. Biol. 35,134-144
153. Yang, T. and Poovaiah, B.W. (2002) Hydrogen peroxide homeostasis: Activation of plant catalase by calcium/calmodulin. Proc. Natl. Acad. Sci. USA 99,4097-4102
154. Yuan Q.P., Quaekenbush J., Sultana R., Pertea M., Salzberg S.L. and Buell C.R. (2001) Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol. 125,1166-1174
155. Yubero-Serrano, E.M., Moyano, E., Medina-Escobar, N. and Munoz-Blanco, J. (2003) Identification of a strawberry gene encoding a non-specific lipid transfer protein that responds to ABA, wounding and cold stress. J. Exp.Bot. 54,1865-1877
156. Zhou J. and Goldsbrough P.B. (1994) Functional homologs of fungal metallothionein genes from Arabidopsis. Plant Cell 6, 875--884
157. Zhu, Y., Maher, E.A., Masoud, S., Dixon, R.A., and Lamb, C.J. (1994). Enhanced protection against fungal attack by constitutive coexpression of chitinase and glueanase genes in transgenic tobacco. Bio/Technology 12, 807-812
2．郭晶心，周乃元，马荣才，曹鸣庆(2003)利用mRNA差别显示技术研究大白菜结球过程中的基因表达 农业生物技术学报 11，456-460
3．严继勇 (2004)BcpLH反义基因在大白菜中的转化及其功能的研究 浙江大学博士学位论文
4．杨素欣，冯献忠，刘平林，何玉科．(2000)甘蓝中BcpLH同源基因的克隆及其表达分析．植物生理学报 26，363-368
5．余旭红，彭洁松，冯献忠，郑志仁，杨素欣，唐向荣，沈瑞娟，刘平林，何玉科．(2000)大白菜包叶特异基因的克隆及其结构特征和表达方式．中国科学(C辑)30，475-482
6．甄志成，姚志建．(2001)毛细管阵列电泳与规模化DNA测序．色谱19，361-364
7. Ablett, E., Seaton, G., Scott, K. and Shelton, D. (2000) Analysis of grape ESTs: global gene expression patterns in leaf and berry. Plant Sci. 159,87-95
8. Adams M.D., Kelley J.K., Gocayne J.D., Dubnick M., Polymeropoulos M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., Kerlavage A.R., McCombie W.R. and Venter J.C. (1991)Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252,1651-1656
9. Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman DJ. (1990) Basic local alignment search tool. J Mol. Biol. 215,403-410
10. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25,3389-3402
11. Allona I., Quinn M., Shoop E., Swope K., Cyr S.S., Carlis J., Riedl J., Retzel E., Campbell M.M., Sederoff R. and Whetten R.W. (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc. Natl. Acad. Sci. USA 95,9693-9698
12. Anderson, I. and Brass, A. (1998) Searching DNA databases for similarities to DNA sequences: when is a match significant? Bioinformatics 14,349-356.
13. Audic, S. and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res. 7,986-995
14. Babula D,, Kaczmarek M., Barakat A., Delseny M., Quiros C.F. and Sadowski J. (2003) Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map. Mol. Gen. Genomics 268,656-665
15. Baker, S.S., Wilhelm, K.S., and Thomashow, M.F. (1994) The 5'-region of Arabidopsis thaliana COR15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol. Biol. 24,701-713
16. Bailey, P.C., Martin, C., Toledo-Ortiz G., Quail, P.H., Huq, E., Heim, M.A., Jakoby, M. and Weisshaar B. (2003) Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana. Plant Cell 15, 2497-2501
17. Barakat, A., Szick-Miranda, K., Chang, I. F. and Guyot, R. (2001) The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol. 127,398-415
18. Baugh L. R., Hill A. A., Brown E. L. and Hunter C.P. (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29,e29
19. Bell C.J., Dixon R.A., Farmer A.D., Flores R., Inman J., Gonzales R.A., Harrison M.J., Paiva N.L., Scott A.D., Weller J.W. and May G.D, (2001) The Medicago Genome Initiative: a model legume database. Nucleic Acids Res. 29(1), 114-117
20. Belyavsky A., Vinogradova T. and Rajewsky K. (1989) PCR-based cDNA library construction: general cDNA libraries at the level of a few cells. Nucleic Acids Res. 17,2919-2932
21. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. and Wheeler D.L. (2003) GeneBank. Nucleic Acids Res. 31, 23-27
22. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. and Wheeler D.L. (2004) GeneBank: update. Nucleic Acids Res. 32, D23-D26
23. Bevan, M., Bancroft, I., Bent, E. and Love, K. (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391,485-488
24. Brady, G.., Barbara, M. and Iscove, N.N. (1990) Representative in vitro cDNA amplication from individual hemopoietic cells and elonies. Methods Mol. Cell. Biol. 2, 17-15.
25. Brady, G. and Iscove, N.N. (1993) Construction of cDNA libraries from single cells. Yeast 225, 611-623.
26. Brandle J.E., Richman A., Swanson A.K. and Chapman B.P. (2002) Leaf ESTs from Stevia rebaudiana: a resource for gene discovery in diterpene synthesis. Plant Mol. Biol. 50,613-622
27. Bryant Z., Subrahmanyan L. and Tworoger M. (1999) Charatedzation of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proc. Natl. Acad Sci. USA 96,5559-5564
28. Broglie, K., Chet, I., Hollyday, M., Cressrnan, R., Biddle, P., Knowlton, S., Mauvais, C.J., and Broglie, R. (1991). Transgenic plants with enhanced resistance to the fungal pathogen Rhizoctonia solani. Science 254, 1194-1197.
29. Buchanan-Wollaston V. (1994) Isolation of cDNA clones for genes that are expressed during leaf senescence in Brassica napus: identification of a gene encoding a senescence-specific metallothionein-like protein. Plant Physiol. 105, 839--846.
30. Buetow K.H., Edmonson M.N. and Cassidy A.B. (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet. 21,323-325
31. Burr B. (2002) Mapping and sequencing the rice genome. Plant Cell 14, 521-523
32. Callis, J. and Vierstra, R.D. (2000) Protein degradation in signaling. Cure. Opin. Plant Biol. 3,381-386
33. Castro, N.C., Gotuzzo, E., Rodriguez, M., and Guerra, H. (2000) Clinical Application of a Dot Blot Test for Diagnosis of Enteric Fever Due to Salmonella enterica Serovar Typhi in Patients with Typhoid Fever from Colombia and Peru. Clinical and Diagnostic Laboratory Immunology 7, 312-313
34. Cato S.A., Gardner R.C., Kent J. and Richardson T.E. (2001) A rapid PCR-based method for genetically mapping ESTs. Theor Appl. Genet. 102,296-306
35. Chenchik, A., Diachenko, L., Moqadam, F., Tarabykin, V., Lukyanov, S. and Siebert, P.D. (1996) Full-Length cDNA Cloning and Determination of mRNA 5' and 3' Ends by Amplification of Adaptor-Ligated cDNA. BioTechniques 21,526-534
36. Choi, D., Kim, H.M., Yun, H.K., Park, J.A., Kim, W.T. and Bok, S.H. (1996) Molecular cloning of a metallonthionein-like gene from Nicotiana glutinosa L. and its induction by wounding and tobacco mosaic virus infection. Plant Physiol. 112,353-359
37. Chou H.H., Holmes M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17,1093-1104
38. Colling, D.B., Kragh, K.M., Mikkelsen, J.D., Nielsen, K.K., Rasmussen, U., and Vad, K. (1993). Plant chitnases. Plant J. 3,31-40
39. Connors B.J., Maynard C.A. and Powell W.A. (2001) Expressed sequence tags from stem tissue of the American chestnut, Castanea dentate. Biotech. Lett. 23,1407-1411
40. Cooke R., Raynal M., Laudie M. and Delseny M. (1997) Identification of members of gene families in Arabidopsis thalana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J. 11,1127-1140
41. Covitz P. A., Smith L.S. and Long S.R. (1998) Expressed sequence tags from a root-hair-enriched Medicago truncatula cDNA library. Plant Physiol. 117,1325-1332
42. del Pozo J.C., Dharmasiri, S., Hellmann, H., Walker, L., Gray, W.M., and Estelle, M. (2002) AXR1-ECR1-dependent conjugation of RUB1 to the Arabidopsis cullin AtCull is required for Auxin response. Plant Cell 14,421-433
43. Delseny M., Cooke R., Raynal M. and Grellet F. (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett. 403,221-224
44. Dixon A.K., Richardson P. J., Lee K., Carter N.P. and Freeman T. C. (1998) Expresion profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Res. 26,4426-4431
45. Duggan D.J., Bittner M., Chen Y.D., Meltzer P. and Trent J.M.(1999) Expression profiling using cDNA microarrays. Nature Gent. 21,10-14.
46. Dunn M. A., Hughes M. A., Zhang L., Pearce R.S., Quigley A.S. and Jack P. L. (1991) Nucleotide sequence and molecular analysis of the low temperature induced cereal gene, BLT4. Mol. Gen. Genet. 229,389-394
47. Eckardt N.A. (2000) Sequencing the rice genome. Plant Cell 12, 2011-2017
48. Epple P., Aple K. and Bohlmann H. (1997) ESTs reveal a multigene family for plant defensisns in Arabidopsis thaliana. FEBS Lett. 400, 168-172
49. Ewing B., Hillier L., Wendl M.C. and Green P. (1998) Base-calling of automated sequencer traces using phred. Accuracy assessment. Genome Res. 8,175-185
50. Ewing R.M., Kahla A.B., Poirot O., Lopez F., Audic S. and Claverie J.M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene espression. Genome Res. 9,950-959
51. Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y., Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S, Tang Y., Weng Q., Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T., Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R., Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G., Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C., Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J., Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J., Li J., Hong G., Xue Y. and Han B. (2002) Sequence and analysis of rice chromosome 4. Nature 420,316-320
52. Fowler, S. and Thomashow, M.F. (2002) Arabidopsis transcriptome profiling indicates that multiple regulatiory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14,1675-1690
53. Gang D.R., Wangg J., Dudareva N., Nam K.H., Simon J.E., Lewinsohn E. and Pichersky E. (2001) An investigation of the storage and biosynesis of phenylpropenes in sweet basil. Plant Physiol. 125,539-555
54. Galat, A. and Metcalfe, S. (1995) Peptidyl prolyl cis-trans isomerases. Prog. Biophys. Mol. Biol. 63, 67-118
55. Genund C., Ramu C., Altenberg-Greulich B. and Gibson T.J. (2001) Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with
eukaryotic gene-sized queries. Nucleic Acids Res. 29,1272-1277
56. Craham, L.S., and Sticklen, M.B. (1994). Plant chitinases. Can. J. Bot. 72, 1057-1083.
57. Gray, W.M., del Pozo, J.C., Walker, L., Hobbie, L., Risseeuw, E., Banks, T., Crosby, W. L., Yang, M., and Estelle, M. (1999) Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. Genes Dev. 13,1675-1691
58. Grivet L., Glaszmann J.C., Vincentz M., da Silva E and Arruda P. (2002) ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes. Theor. Appl. Genet. 106, 190-197
59. Gyorgyey J., Vaubert D., Jimenez-Zurdo J.I., Charon C., Troussard L., Kondorosi A. and Kondorosi E. (2000) Analysis ofMedicago truncatula nodule expressed sequence tags. Mol. Plant-Microbe Inter. 13,62-71
60. Hatey F., Tosser-Klopp G., Clouscard-Martinato C., Mulsant P. and Gasser F. (1998) Expressed sequence tags for genes: a review. Genet Sel. Evol. 30,521-541
61. Hays D.B. and Skinner D.Z. (2001) Development of an expressed sequence tag (EST) library for Medicago sativa. Plant Sci. 161,517-526
62. Hellmann, H. and Estelle, M. (2002) Plant development: regulation by protein degradation. Science 297,793-797
63. He, Y.K., Xue, W.X., Sun, Y.D., Yu, X.H. and Liu, P.L. (2000) Leafy head formation of the progenies of transgenic plants of Chinese cabbage with exogenous auxin genes. Cell Res. 10,151-60
64. Hofte H., Desprez T., Amselem J., Chiapello H., Rouze P., Caboche M., Moisan A., Jourjon M.F., Charpenteau J.L., Berthomieu P., Guerrier D., Giraudat J., Quigley F., Yu D.Y., Mache R., Raynal M., Cooke R., Grellet F., Delseny M., Parmentier Y., de Marcillac G., Gigot C., Fleck J., Philipps G., Axelos M., Bardet C., Tremousayue D. and Lescure B. (1993) An inventory of 1152 expressed sequence tags obtained by partial Sequencing of cDNAs from Arabidopsis thaliana. Plant J. 4,1051-1061
65. Hsiung, W.G., Chang, H.C., Pellequer, J.L., La Valle, R., Lanker, S., and Wittenberg, C. (2001) F-box protein Grrl interacts with phosphorylated targets via the cationic surface of its leucine-rich repeat. Mol. Cell. Biol. 19, 989-1001
66. Huang X.Q. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9,868-877
67. Iqbal, M.J., Yaegashi, S., Njiti, V.N. and Absan, R. (2002) Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f.sp. glycines. Mol. Genct. Genomics 268,407-417
68. Iscove, N.N., Barbara, M., Gu, M., Gibson, M., Modi, C. and Winegarden, N.(2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 20, 940-943.
69. Ito H, Kato T. (1957) Studies on the head formation of Chinese cabbage: histological and physiological studies of head formation. J. Jpn. Soc. Hortic. Sci. 26,154-204
70. Jach, Q, Grnhardt, B., Mundy, J., Logemann, J., Pinsdorf, E., Leah, R., Schell, J., and Maas, C. (1995) Enhanced quantitative resistance against fungal disease by combinatorial expression of different barley antifungal proteins in transgenic tobacco. Plant J. 8, 97-109.
71. Jain, A.K.(2001) Identification of drought-responsive transcripts in peanut (Arachis hypogaea L.) Elect. J. Biotechnol. 4,59-67
72. Jiang, C., Iu, B., and Singh, J. (1996) Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol. Biol. 30,679-684
73. Jones D.T. and Swindells M.B. (2002) Getting the most from PSI-BLAST. Trends Biochem. Sci. 27, 161-164
74. Joshi, C.P. (1987) An inspection of the domain between putative TATA box and translation start site in 79 plants. Nucleic Acids Res. 15,6643-6653
75. Jung, S.H., Lee, J.Y., and Lee, D.H. (2003) Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol.Biol. 52,553-567
76. Kanaya, E., Nakajima, N., Morikawa, K., Okada, K. and Shimura, Y. (1999) Characterization of the transcriptional activator CBF1 from Arabidopsis thaliana. J. Biol. Chem. 274,16068-16076
77. Kenzelmann M., Klaren R., Hergenhahn M., Bonrouhi M., Grone H.J., Schmid W. and Schutz G. (2004) High-accuracy amplification of nanogrm total RNA amounts for gene profiling. Genomics 83,550-558
78. Kepinski, S. and Leyser, O. (2002) Ubiquitination and auxin signaling: A degrading story. Plant Cell S81-S95
79. Kim, G.T. and Tsukaya, H. (2002) Regulation of the biosynthesis of plant hormones by cytochrome P450s. J.Plant Res. 115,169-177
80. Kitashiba,H., Iwai, T., Toriyama, K., Watanabe, M. and Hinata, K. (1996) Identification of genes expressed in the shoot apex of Brassica campestris during floral transition. Sex Plant Reprod 9,186-188
81. Knight, H., Trewavas A.J. and Knight M.R. (1996) Cold Calcium Signaling in Arabidopsis Involves Two Cellular Pools and a Change in Calcium Signature after Acclimation. Plant Cell 8,489-503
82. Kota R, Varshney RK, Thiel T, Dehmer KJ and Graner A. (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgate L.). Hereditas 135,145-151
83. Kreps, J. A., Wu, Y., Chang, H. S. and Zhu, T. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130,2129-2141
84. Krishna, P., Sacco, M., Cherutti, J.F. and Hill, S. (1995) Cold-Induced Accumulation of hsp90 Transcripts in Brassica napus. Plant Physiol. 107,915-923
85. Kwak J.M., Kim S.A., Hong S.W. and Nam H.G. (1997) Evaluation of 515 expressed sequence tags obtained from guard cells of Brassica campestris. Planta 202,9-17
86. Lan T.H., DelMonte T.A., Reisehmann K.P., Hyman J., Kowalski S.P., McFerson J., Kresovich S. and Paterson A.H. (2000) An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res. 10,776-788
87. Lee, J.Y. and Lee D.H. (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol. 132,517-529
88. Liang F., Holt I., Pertea G., Karamycheva S., Saizberg S.L. and Quackenbush J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28,3657-3665
89. Liang P. and Pardee A.B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257,967-971
90. Lim, C.O., Kim, H.Y., Kim, M.G., Lee, S.I., Chung, W.S., Park, S.H., Hwang, I. and Cho, M.J. (1996) Expressed sequence tags of Chinese cabbage flower bud cDNA. Plant Physiol. 111,577-588
91. Lim, J.Y.., Shim, C.S., Chung, E.J., Kim, J.S., Kim, H.U., Oh, S.J., Choi, W.B., Ryou, C.S., Kim, J.B., Kwon, M.S., Chung, T.Y., Song, S.I., Kim, J.K., Nahm, B.H., Hwang, Y.S., Eun, M.Y., Lee, J.S., Cheong, J.J. and Choi, Y.D. (2000) Analysis of expressed
sequence tags from Brassica rapa L.ssp.pekinensis. Mol.Cells 10,399-404
92. Lin, X.Y., Kaul, S., Rounsley, S., Shea, T.E, Benito, M.I., Town, C.D., Fujii, C.Y., Mason, T., Bowman, C.L., Barnstead, M., Feldblyum, T.V., Buell, C.R., Ketchum, K.A., Lee, J., Ronning, C.M., Koo, H.L., Moffat, K.S., Cronin, L.A., Shen, M., Pai, G., Aken, S.V., Umayam, L., Tallon, L.J., Gill, J.E., Adams, M.D., Carrera, A.J., Creasy, T.H., Goodman, H.M., Somerville, C.R., Copenhaver, G. P., Preuss, D., Nierman, W.C., White, O., Eisen, J.A., Salzberg, S.L., Fraser, C.M. and Venter, J.C.. (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768
93. Liu J.Y., Hara C., Umeda M., Zhao Y., Okita W. and Uchimiya H. (1995) Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L.): evaluation of expressed sequence tags, and expression levels of mRNAs. Plant Mol. Biol. 29,685-689
94. Lonsdale D., Crowe M., Arnold B. and Arnold B.C. (2001) Mendel-GFDb and Mendel-ESTs: databases of plant gene families and ESTs annotated with gent family numbers and gene family names. Nucleic Acids Res. 29,120-122
95. Luo M., Kong X.Y., Jiang T., Jia C., Zhou R.H., Jia J.Z. (2002) Analysis of resistance to powdery mildew in wheat based on expressed sequence tags (EST) technique. Acta Botanica Sinica 44,567-572
96. Martin K.J. and Pardee A.B. (2000) Identifying expressed genes. Proc. Natl. Acad. Sci. USA 97,3789-3791
97. Meinke D.W., Cherry J.M., Dean C.D., Rounsley S. and Koornneef M. (1998) Arabidopsis thaliana: a model plant for genome analysis. Science 282,662-682
98. Medina, F.J., Cerdido, A., and de Caxcer, G. (2000) The functional organization of the nucleolus in proliferating plant cells. Eur. J. Histochem. 44,117-131
99. Michalek W, Weschke W, Pleissner KP and Graner A. (2002) EST analysis in barley defines a unigene set comprising 4000 genes. Theor. Appl. Genet. 104,97-103
100. Murphy, A. and Taiz, L. (1995) Compadsion of metallothionein gene expression and nonprotein thiols in ten Arabidopsis ecorypes. Plant Physiol. 109,945-954
101. Neven, L.G., Haskell, D.W., Guy, C.L., Denslow, N., Klein, P.A., Green, L.G. and Silverman, A. (1992) Association of 70-kilodalton heat-shock cognate proteins with acclimation to cold. Plant Physiol. 99,1362-1369
102. Newman, T., Bruijn, F.J.D., Green, P., Keegstra, K, Kende, H., McIntosh, L., OhIrogge, J., Raikhel, N.,, Somerville, S., Thomashow, M., Retzel, E. and Somerville, C. (1994) Genes galore: A summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106,1241-1255
103. Nikaldo I., Asamizu E., Nakajima M., Nakamura Y., Saga N. and Tabata S. (2000) Generation of 10154 expressed sequence tags from a leafy gametophyte of a marine Red Alga, Porphyra yezoensis. DNA Res. 7,223-227
104. Ohlrogge J. and Benning C. (2000) Unraveling plant metabolism by EST analysis. Curr. Opin. Plant Biol. 3,224-228
105. Olson M., Hood L., Cantor C. and Botstein D. (1989) A common language for physical mapping of the human genome. Science 245,1434-1435
106. Oweas-Grillo, J.K., Hofman, K., Hutchison, K.A., Yem, A.W., Deibel, M.R., Handschumacher, J.R.E. and Pratt, W.B. (1995) The cyclosporine A-binding immunophilin Cyp-40 and the FK506-binding immunophilin HSP56 bind to a common site on HSP90 and exist in independent cytosolie heterocomplexes with the untransformed glucocorticoid receptor. J Biol Chem 270, 20479-20484
107. Puskas L.G., Zvara A., Hackler L., Jr and Van Hummelen P. (2002) RNA
amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32,1330-1340
108. Petalidis L., Bhattacharyya S., Morris G.A., Collins V.P., Freeman T.C. and Lyons P.A. (2003) Global amplification of mRNA by template-swiching PCR: linearity and applification to microarray analysis. Nucleic Acids Res. 31, e142
109. Pickart, C.M. (2001) Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503-533
110. Picoult-Newberg L., Ideker T.E., Pohl M.G., Taylor S.L., Donaldson M.A., Nickerson D.A.and Boyce-Jacino M. (1999) Mining SNPs from EST databases. Genome Res. 9,167-174
111. Provart, N.J., Gil, P., Chen, W. and Han, B. (2003) Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures. Plant Physiol. 132,893-906
112. Qin L., Prins P., Jones J.T., Popeijus H., Smant G., Bakker J. and Helder J. (2001) GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP. Nucleic Acids Res. 29,1616-1622
113. Quackenbush J., Cho J., Lee D., Liang F., Holt I., Karamycheva S., Parvizi B., Pertea G., Sultana R. and White J. (2001) The TIGR Gene Indices: analysis of gene transcript sequences in higly sampled eukaryotic species. Nucleic Acids Res. 29,159-164
114. Reichler, S.A., Balk, J., Brown, M. E., Woodruff, K. (2001) Light differentially regulates cell division and the mRNA abundance of pea nucleolin during de-etiolation. Plant Physiol. 125,339-350
115. Ronning C.M., Stegalkina S.S., Ascenzi R.A., Bougri O., Hart A.L., Utterbach T.R., Vanaken S.E., Riedmuller S.B., White J.A., Cho J., Pertea G.M., Lee Y.D., Karamycheva S., Sultana R., Tsai J., Quackenbush J., Griffiths H.M., Restrepo S., Smart C.D., Fry W.E., der Hoeven R.V., Tanksley S., Zhang P.F., Jin H.L., Yamamoto M.L., Baker B.J. and Buell CR. (2003) Comparative analyses of Potato expressed sequence tag libraries. Plant Physiol. 131,419-429
116. Ruan Y.J., Gilmore J. and Conner T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15,821-833
117. Saghizadeh M., Brown D. J., Tajbakhsh J., Chen Z., Kenney C., Farber D.B. and Nelson S.F. (2003) Evaluation of techniques using amplified nucleic acid probes for gene expression profiling. Biomol. Eng. 20,97-106
118. Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Blacker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech E, De S., V., Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Querier F., Schafer M., Muller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Lohnert T.H., Nordsiek G, Reichelt J., Scharfe M., Schon O., Bargues M., Terol J., Climent J., Navarro E, Collado C., Perez-Perez A., Ottenwalder B., Duehemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.P., Cottet A., Casacuberta E., Monfort A., Argiriou A., flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., School H., Rudd S., Zaccaria P., Mewes H.., Mayer K.F., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G,
Militscher J., Sellers E, Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M. and Tabata S. (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408, 820-822
119. Sasaki T., Song J.Y., Ban Y.K., Matsui E., Fang F., Higo H., Nagasaki H., Hori M., Miya M., Kayano E.M., Takiguchi T., Takasuga A., Niki T., Ishimaru K., Ikeda H., Yamarnoto Y., Mukai Y., Ohta I., Miyadera N., Havukkala I. and Minobe Y. (1994) Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus eDNA library. Plant J. 6,615-624
120. Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H., Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M., Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A, Kamiya K., Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K., Waki K, Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.I., Eun M.Y., Yano M., Jiang J. and Gojobori T. (2002) The genome sequence and structure of rice chromosome 1. Nature 420, 312-316
121. Scott K.D., Eggler P., Seaton G, Rossetto M., Ablett E.M., Lee L.S. and Henry R.J. (2000) Analysis of SSRs derived from grape ESTs. Theor. Appl. Genet. 100,723-726
122. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K. (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13,61-72
123. Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Caminci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A. and Shinozaki K. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296,141-145
124. Seth D., Correll M.D., McGuinness P.H. Leo M.A., Lieber C.S., MeCaughan G.W. and Haber P.S. (2003) SMART amplification maintains representation of relative gene expression: quantitative validation by real time PCR and application to studies of alcoholic liver disease in primates. J. Biochem. Biophys. Methods 55,53-66
125. Shen, B., Carneiro, N., Torres-Jerez, I., Stevenson, B. (1994) Partial sequencing and mapping of clones from two maize cDNA libraries. Plant Mol.Biol. 26,1085-1101
126. Smith L., Underhill P., Pritchard C., Tymowska-Latanne Z., Abdul-Hussein S., Hilton H., Winchester L., Williams D., Freeman T., Webb S. and Greenfield A. (2003) Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res. 31,e9
127. Sota A., Allona, I., Collada, C., Guevara, M.A., Casado, R., Cerezo, E.R., Aragoncillo, C. and Gomez L. (1999) Heterologous expression of a plant small heat-shock protein enhances Escherichia coli viabiligy under heat and cold stress. Plant Physiol. 120,521-528
128. Sutton, G, White, O., Adams, M., and Kerlavage, A. (1995) TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Science & Technology 1,9-19
129. Sterky F., Regan S., Karlsson J., Hertzberg M., Rohde A., Holmberg A., Amini B., Bhalerao R., Larsson M., Villarroel R., Montagu M.V., Sandberg G., Olsson O., Teeri T.T., Boerjan W., Gustafsson P., Uhlen M., Sundberg B. and Lundcrbcrg J. (1998) Gone discovery in the wood-forming tissue of poplar: analysis of 5692 expressed sequence tags. Proc. Natl. Acad Sci. USA 95,13330-13335
130. Stockinger, E.J., Gilmour, S.J., and Thomashow, M.F. (1997) Arabidopsis thaliana CBF1 enoodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl. Acad. Sci. USA 94,1035-1040
131. Stump, M.D., Cherry J.L. and Weiss R.B. (1999) The use of modified palmers to eliminate cycle sequencing artifacts. Nucleic Acids Res. 27,4642-4648
132. Tabaei-Aghdaei, S.R., Pearce, R.S., and Harrison, P. (2003) Sugars regulate cold-induced gene expression and freezing-tolerance in barley cell cultures. J. Exp.Bot. 54,1565-1575
133. Thtiharju, S., Sangwan V., Monroy, A.F., Dhindsa, R.S. and Borg M. (1997) The induction of kin genes in cold-acclimating Arabidopsis thaliana. Evidence of a role for calcium. Planta 203,442-447
134. Thiel T., Michalek W., Varshney K. and Graner A. (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgate L.). Theor. Appl. Genet. 106,411-422
135. Thomas, D.J., Thomas, J.B., Prier, S.D., Nasso, N. E. and Herbert S. K. (1999) Iron Superoxide Dismutase Protects against Chilling Damage in the Cyanobacterium Synechococcus species PCC7942. Plant Physiol. 120,275-282
136. Trevio M.B. and Connell M.A. (1998) Three Drought-Responsive Members of the Nonspecific Lipid-Transfer Protein Gene Family in Lycopersicon pennellii Show Different Developmental Patterns of Expression. Plant Physiol. 116, 1461-1468
137. Trumper L.H., Brady G. and Bagg A. (1993) Single-cell analysis of Hodgkin and Reed-Sternberg cells: molecular heterogeneity of gene expression and p53 mutations. Blood 81,3097-3115
138. Trumper L.H., Brady G., Vicini S., Cossman J. and Mak T.W. (1992) Gene expression in single Reed-Sternberg cells of Hodgkin's disease: results from PCR-generated single-cell cDNA libraries. Ann. Oncol. 3 (suppl 4),25-26
139. Tsang, W.T., Bowler, C., Camp, H. D., Villarroel, W.V.R., Genetello, C., Montagu, M.V. and Inze D. (1991) Differential Regulation of Superoxide Dismutases in Plants Exposed to Environmental Stress. Plant Cell 3,783-792
140. Tuteja, R. and Tuteja, N. (1998) Nucleolin: a multifunctional major nuclcolar phosphoprotein. Crit. Rev.Biochem.Mol.Biol. 33,407-436
141. Velculescu V.E., Zhang L., Vogelstein B. and Kinzler K.W. (1995) Serial analysis of gene expression. Science 270, 484-487
142. Vierstra, R.D. (2003) The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends in Plant Sci. 8,135-142
143. Voiblet, C., Duplessis, S., Encelot, N., and Martin, F. (2001) Identification of symbiosis-regulated genes in Eucalyptus globules-Pisolithus tinctorius ectomycorrhiza by differential hybridization of arrayed cDNAs. Plant J. 25,181-191
144. Wang E., Miller, L. D., Ohnmaeht, G A., Liu E. T. and Marincola F. M. (2000) High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18,457-459
145. Wang W., Wyekof J.B., Wang Y., Bottinger E.P., Segall J.E. and Condeelis J.S. (2003) Gene expression analysis on small numbers of invasive cells collected by chemotaxis from primary mammary tumors of the mouse. BMC Biotechnol. 3,13-24
146. Wheeler D.L., Church D.M., Federhen S., Lash A.E., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E., Tatusova T.A. and Wagner L. (2003) Database resources of the national center for biotechnology. Nucleic Acids Res. 31,28-33
147. White J.A., Todd J., Newman T., Foeks N., Girke T., De Harduya O.M., Jaworski J.G., Ohlrogge J.B. and Benning C. (2000) A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol. 124,1582-1594
148. Wirtz K.W.A. and Cradella T.W.J. (1990) Properties and modes of action of specific and nonspecifie phospholipid transfer proteins. Experientia 46, 592-599
149. Wortey, C.K., Zenser, N., Ramos, J., Rouse, D., Leyser, O., Theologis, A., and Callis, J. (2000) Degradation of Aux/IAA proteins is essential for normal auxin signaling. Plant J. 21,553-562
150. Xue, G. P. (2002) An AP2 domain transcription factor HvCBF1 activates expression of cold-res-ponsive genes in barley through interaction with a (G/a)(C/t)CGAC motif. Biochim.Biophys.Acta 1577,63-72
151. Xue, G..P. and Loveridge, C.W. (2004) HvDRF1 is involved in abseisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element. Plant J. 37,326-339
152. Yamamoto K and Sasaki T. (1997) Large-scale EST sequencing in rice. Plant Mol. Biol. 35,134-144
153. Yang, T. and Poovaiah, B.W. (2002) Hydrogen peroxide homeostasis: Activation of plant catalase by calcium/calmodulin. Proc. Natl. Acad. Sci. USA 99,4097-4102
154. Yuan Q.P., Quaekenbush J., Sultana R., Pertea M., Salzberg S.L. and Buell C.R. (2001) Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol. 125,1166-1174
155. Yubero-Serrano, E.M., Moyano, E., Medina-Escobar, N. and Munoz-Blanco, J. (2003) Identification of a strawberry gene encoding a non-specific lipid transfer protein that responds to ABA, wounding and cold stress. J. Exp.Bot. 54,1865-1877
156. Zhou J. and Goldsbrough P.B. (1994) Functional homologs of fungal metallothionein genes from Arabidopsis. Plant Cell 6, 875--884
157. Zhu, Y., Maher, E.A., Masoud, S., Dixon, R.A., and Lamb, C.J. (1994). Enhanced protection against fungal attack by constitutive coexpression of chitinase and glueanase genes in transgenic tobacco. Bio/Technology 12, 807-812