阿拉善荒漠区珍稀泌盐植物长叶红砂响应盐胁迫的转录组学研究
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摘要
长叶红砂(Reaumuria trigyna)是内蒙古东阿拉善-西鄂尔多斯地区特有的双子叶泌盐盐生小灌木,具有适应盐渍荒漠环境的独特形态特征和生理调控机制,是研究植物耐盐机理、获得耐盐优异基因的好材料。然而,由于遗传信息的缺乏,使得针对该植物耐盐分子机理的研究进展缓慢。本研究利用Illumina测序技术对正常生长(C21)和盐胁迫处理(T43)的长叶红砂进行转录组深度测序,获得了该植物大量的表达基因信息,分析了其响应盐胁迫的转录组水平变化,探讨了离子平衡调节及活性氧清除系统在该植物盐胁迫响应过程中发挥的作用；此外,尝试了利用DDRT-PCR (Differential Display Reverse Transcription PCR)技术从海量转录组数据中快速筛选盐胁迫诱导基因的方法,并在所得转录组数据中进行了SSR (Simple Sequence Repeat)位点的识别和初步验证。研究结果如下：
1.经测序,C21和T43样本分别得到约2651.3和2816.7万条测序读长(Read),总数据量超过5G,搭建了长叶红砂转录组信息平台；去除低质量读长后,两数据库中分别有92.65%和92.54%条读长错误出现率为1%(Q20),可用于后续转录组的从头(de novo)组装。
2.经de novo组装,两数据库的高质量读长分别被组装为68076(C21)和71194(T43)条Unigenes;对上述序列做进一步拼接和去冗余,最终得到65340条All-Unigenes;其中,35459(52.27%)条Unigenes与公共蛋白数据库中已报道的基因有较高同源性,13552条Unigenes被注释到44个GO (Gene Ontology)条目中,10968条Unigenes被注释到25个COG (Clusters of Orthologous Groups)基因簇中,15995Unigenes被注释到119个KEGG (Kyoto Encyclopedia of Genes and Genomes)代谢通路中；RT-PCR验证结果表明,随机挑选的30条Unigenes中,26条能扩增出预期长度的cDNA片段,功率为86.7%。
3. Unigene表达量注释和差异基因表达分析显示：65340条Unigenes中,共有64694条在盐胁迫前后的表达量发生了变化,包括上调基因32697条和下调基因31997条；5032Unigenes为显著差异表达基因(Differentially Expressed Gene, DEG),包括2370条上调DEGs和2662条下调DEGs,1947条DEGs富集分布在27个GO条目中,2086条DEGs富集分布在33个KEGG代谢通路中；在Unigene注释结果中,共有135、72和25条Unigenes被注释为K+吸收、H+运输及Na+外排基因,298条Unigenes为活性氧清除系统相关基因,结合它们的表达模式探讨了离子平衡调节和活性氧清除系统在长叶红砂盐胁迫响应中发挥的作用；30条随机挑选Unigenes的qRT-PCR检测结果与它们的数字基因表达计算数据基本一致。
4.利用DDRT-PCR技术结合本地比对分析快速从海量转录组数据库中筛选耐盐基因。经qRT-PCR验证,DDRT-PCR分离得到的18条基因的表达模式与它们的数字基因表达量注释结果高度一致,可作为下一步深入研究该植物耐盐分子机制的候选基因。
5.在65340条Unigenes中共发现225种、6215个简单重复序列,出现频率为10%；4153条Unigenes可设计出SSR扩增引物,成功率为66.82%；220对随机挑选的SSRs引物中,217对能扩增出PCR产物。
Reaumuria trigyna is an endangered small shrub endemic to the Eastern Alxa-Western Ordos area in Inner Mongolia. This dicotyledonous recretohalophyte has developed unique morphological characteristics and adaption stratigies that allow it to tolerate the stress imposed by semi-desert saline soil. The remarkable capabilities to tolerance salty soil make it excellent candidates to investigate salt-tolerance mechanisms and to identify effective salt-response genes in the plant. However, it is impossible to explore the molecular mechanisms underlying this tolerance without detailed genomic information. At the present study, two sequencing libraries prepared from control (C21) and NaCl-treated samples (T43) were sequenced using short reads sequencing technology (Illumina) to obtain the transcriptome information of R. trigyna, and to investigate changes in the transcriptome of the species in response to salt stress. Based on the RNA-seq data, possible roles of the ion homeostasis regulation and the reactive oxygen species (ROS) scanvenging system played in salt stressed R. trigyna were discussed. In addition, DDRT-PCR technique was attemped to rapidly identify salt-stress induced genes from the massive amount of transcriptome sequencing data. Simple sequence repeat (SSR) locis were mined and validated. The results of the present study are as follow:
1. In total,26.51and28.17million raw reads were generated from C21and T43libraries, respectively. The overall sequencing outputs were over than5Gigabase, and the transcriptome data platform was constructed. Among all the raw reads,more than92%had Phred-like quality scores at the Q20level (an error probability of1%). These were used for de novo assembly.
2.68076(C21) and71194(T43) Unigenes were assembled from the Clean reads of two transcriptomes. After removal of redundancy,65340All-Unigene were clusted by combining C21-and T43-Unigenes. Among65340Unigenes,35495(52.27%) showed significant BLAST hits in the public databases.13552Unigenes were categorized into44Gene Ontology (GO) terms,10968Unigenes were subjected to25Clusters of Orthologous Groups (COG) families, and35271Unigenes were mapped to119canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Among the30randomly selected Unigenes,26Unigenes yielded expected fragments and the other four failed to produce amplification products, yielding a success rate of86.7%.
3. Digital gene expression annotation and expression pattern of the differentially expressed genes showed that, among A11-Unigenes,32697were up-regulated and31997were down-regulated upon treatment of R. trigyna seedlings with salt solution.5032significantly differentialy expressed genes (DEGs) were identified, including2370up-and2662down-regulated DEGs.1947DEGs were enriched in27GO terms, and2086DEGs were enriched in33metabolic pathways. Among the Unigenes,135, 72, and25genes were identified to be related to regulation of K+uptake, H+pumping, and Na+efflux, and298Unigenes were predicted to encode antioxidative enzymes related to ROS scavenging. According to the gene expression patterns, the possible role played of the ion homeostasis regulation and the ROS scavenging system in response to salt stress of R. trigyna were discussed. The expression patterns of30randomly selected genes resulted from quantitative reverse transcription PCR (qRT-PCR) were basically consistent with their transcript abundance changes identified by RNA-seq.
4. Rapidly identified the salt-stress induced genes from the massive amount of transcriptome sequencing data by DDRT-PCR combined with local BLAST analysis. The expression patterns of the18genes identified by DDRT-PCR detected by qRT-PCR were highly consistent with the digital gene expression data for the transcriptome database.
5.225SSR motifs and6215SSRs were searched in65340Unigenes with the occurrence frequency of10%. Among Unigenes containing SSR locis,4153were successfully designed with the PCR primers, with the uccessfully rate of66.82%. PCR experiments showed that217of220randomly selected primer pairs could be yealied expected PCR products.
1.经测序,C21和T43样本分别得到约2651.3和2816.7万条测序读长(Read),总数据量超过5G,搭建了长叶红砂转录组信息平台；去除低质量读长后,两数据库中分别有92.65%和92.54%条读长错误出现率为1%(Q20),可用于后续转录组的从头(de novo)组装。
2.经de novo组装,两数据库的高质量读长分别被组装为68076(C21)和71194(T43)条Unigenes;对上述序列做进一步拼接和去冗余,最终得到65340条All-Unigenes;其中,35459(52.27%)条Unigenes与公共蛋白数据库中已报道的基因有较高同源性,13552条Unigenes被注释到44个GO (Gene Ontology)条目中,10968条Unigenes被注释到25个COG (Clusters of Orthologous Groups)基因簇中,15995Unigenes被注释到119个KEGG (Kyoto Encyclopedia of Genes and Genomes)代谢通路中；RT-PCR验证结果表明,随机挑选的30条Unigenes中,26条能扩增出预期长度的cDNA片段,功率为86.7%。
3. Unigene表达量注释和差异基因表达分析显示：65340条Unigenes中,共有64694条在盐胁迫前后的表达量发生了变化,包括上调基因32697条和下调基因31997条；5032Unigenes为显著差异表达基因(Differentially Expressed Gene, DEG),包括2370条上调DEGs和2662条下调DEGs,1947条DEGs富集分布在27个GO条目中,2086条DEGs富集分布在33个KEGG代谢通路中；在Unigene注释结果中,共有135、72和25条Unigenes被注释为K+吸收、H+运输及Na+外排基因,298条Unigenes为活性氧清除系统相关基因,结合它们的表达模式探讨了离子平衡调节和活性氧清除系统在长叶红砂盐胁迫响应中发挥的作用；30条随机挑选Unigenes的qRT-PCR检测结果与它们的数字基因表达计算数据基本一致。
4.利用DDRT-PCR技术结合本地比对分析快速从海量转录组数据库中筛选耐盐基因。经qRT-PCR验证,DDRT-PCR分离得到的18条基因的表达模式与它们的数字基因表达量注释结果高度一致,可作为下一步深入研究该植物耐盐分子机制的候选基因。
5.在65340条Unigenes中共发现225种、6215个简单重复序列,出现频率为10%；4153条Unigenes可设计出SSR扩增引物,成功率为66.82%；220对随机挑选的SSRs引物中,217对能扩增出PCR产物。
Reaumuria trigyna is an endangered small shrub endemic to the Eastern Alxa-Western Ordos area in Inner Mongolia. This dicotyledonous recretohalophyte has developed unique morphological characteristics and adaption stratigies that allow it to tolerate the stress imposed by semi-desert saline soil. The remarkable capabilities to tolerance salty soil make it excellent candidates to investigate salt-tolerance mechanisms and to identify effective salt-response genes in the plant. However, it is impossible to explore the molecular mechanisms underlying this tolerance without detailed genomic information. At the present study, two sequencing libraries prepared from control (C21) and NaCl-treated samples (T43) were sequenced using short reads sequencing technology (Illumina) to obtain the transcriptome information of R. trigyna, and to investigate changes in the transcriptome of the species in response to salt stress. Based on the RNA-seq data, possible roles of the ion homeostasis regulation and the reactive oxygen species (ROS) scanvenging system played in salt stressed R. trigyna were discussed. In addition, DDRT-PCR technique was attemped to rapidly identify salt-stress induced genes from the massive amount of transcriptome sequencing data. Simple sequence repeat (SSR) locis were mined and validated. The results of the present study are as follow:
1. In total,26.51and28.17million raw reads were generated from C21and T43libraries, respectively. The overall sequencing outputs were over than5Gigabase, and the transcriptome data platform was constructed. Among all the raw reads,more than92%had Phred-like quality scores at the Q20level (an error probability of1%). These were used for de novo assembly.
2.68076(C21) and71194(T43) Unigenes were assembled from the Clean reads of two transcriptomes. After removal of redundancy,65340All-Unigene were clusted by combining C21-and T43-Unigenes. Among65340Unigenes,35495(52.27%) showed significant BLAST hits in the public databases.13552Unigenes were categorized into44Gene Ontology (GO) terms,10968Unigenes were subjected to25Clusters of Orthologous Groups (COG) families, and35271Unigenes were mapped to119canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Among the30randomly selected Unigenes,26Unigenes yielded expected fragments and the other four failed to produce amplification products, yielding a success rate of86.7%.
3. Digital gene expression annotation and expression pattern of the differentially expressed genes showed that, among A11-Unigenes,32697were up-regulated and31997were down-regulated upon treatment of R. trigyna seedlings with salt solution.5032significantly differentialy expressed genes (DEGs) were identified, including2370up-and2662down-regulated DEGs.1947DEGs were enriched in27GO terms, and2086DEGs were enriched in33metabolic pathways. Among the Unigenes,135, 72, and25genes were identified to be related to regulation of K+uptake, H+pumping, and Na+efflux, and298Unigenes were predicted to encode antioxidative enzymes related to ROS scavenging. According to the gene expression patterns, the possible role played of the ion homeostasis regulation and the ROS scavenging system in response to salt stress of R. trigyna were discussed. The expression patterns of30randomly selected genes resulted from quantitative reverse transcription PCR (qRT-PCR) were basically consistent with their transcript abundance changes identified by RNA-seq.
4. Rapidly identified the salt-stress induced genes from the massive amount of transcriptome sequencing data by DDRT-PCR combined with local BLAST analysis. The expression patterns of the18genes identified by DDRT-PCR detected by qRT-PCR were highly consistent with the digital gene expression data for the transcriptome database.
5.225SSR motifs and6215SSRs were searched in65340Unigenes with the occurrence frequency of10%. Among Unigenes containing SSR locis,4153were successfully designed with the PCR primers, with the uccessfully rate of66.82%. PCR experiments showed that217of220randomly selected primer pairs could be yealied expected PCR products.
引文
[1]Allakhverdiev S.I, Sakamoto A., Nishiyama Y., et al. Ionic and osmotic effects of NaCl-induced inactivation of photosystems I and II in Synechococcus sp. Plant physiology [J],2000,123(3): 1047-1056.
[2]Ashraf M., Wu DL. Breeding for salinity tolerance in plants [J]. Critical Reviews in Plant Sciences,1994,13(1):17-42.
[3]赵可夫,冯立田.中国盐生植物资源[M].1998,北京：科学出版社.
[4]王宝山,赵可夫,邹琦.作物耐盐机理研究进展及提高作物抗盐性的对策[J].植物学通报,1997,14(1)：25-30.
[5]Zhu JK. Salt and drought stress signal transduction in plants [J]. Annual Review of Plant Biology, 2002,53:247.
[6]Zhu JK. Regulation of ion homeostasis under salt stress [J]. Current Opinion in Plant Biology, 2003,6(5):441-445.
[7]Abogadallah GM. Antioxidative defense under salt stress [J]. Plant Signal Behavior,2010,5(4): 369-374.
[8]Vinocur B., Altman A. Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations [J]. Current Opinion in Biotechnology,2005,16(2):123-132.
[9]Tuteja N. Mechanisms of high salinity tolerance in plants [J]. Methods in Nnzymology,2007, 428:419.
[10]Flowers T., Troke P., Yeo A. The mechanism of salt tolerance in halophytes [J]. Annual Review of Plant Physiology,1977,28(1):89-121.
[11]Greenway H., Munns R. Mechanisms of salt tolerance in nonhalophytes [J]. Annual Review of Plant Physiology,1980,31(1):149-190.
[12]Yamaguchi T., Blumwald E. Developing salt-tolerant crop plants:challenges and opportunities [J]. Trends in Plant Science,2005,10(12):615-620.
[13]Gaxiola R.A., Li J, Undurraga S., et al. Drought-and salt-tolerant plants result from overexpression of the AVP1 H+-pump [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(20):11444-11449.
[14]Pasapula V., Shen G, Kuppu S., et al. Expression of an Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) in cotton improves drought-and salt tolerance and increases fiber yield in the field conditions [J]. Plant Biotechnology Journal 2011,9(1):88-99.
[15]Li Z, Baldwin C.M., Hu Q, et al. Heterologous expression of Arabidopsis H+-pyrophosphatase enhances salt tolerance in transgenic creeping bent grass (Agrostis stolonifera L.) [J]. Plant, Cell & Environment,2009,33(2):272-289.
[16]Xue ZY, Zhi DY, Xue GP, et al. Enhanced salt tolerance of transgenic wheat (Tritivum aestivum L.) expressing a vacuolar Na+/H+antiporter gene with improved grain yields in saline soils in the field and a reduced level of leaf Na+[J]. Plant Science,2004,167,849-859.
[17]Yin XY, Yang AF, Zhang KW, et al. Production and analysis of transgenic maize with improved salt tolerance by the introduction of AtNHXl gene [J]. Acta Botanica Sinica,2004,46(7): 854-861.
[18]Zhang HX, Blumwald E. Transgenic salt-tolerant tomato plants accumulate salt in foliage but not in fruit [J]. Nature Biotechnology,2001,19(8),765-768.
[19]Wu L.Q., Fan Z.M., Qu L.J. et al. Overexpression of the bacterial nhaA gene in rice enhances salt and drought tolerance [J]. Plant Science,2005,168(2):297-302.
[20]Qiu QS, Guo Y, Quintero F.J., et al. Regulation of vacuolar Na+/H+exchange in Arabidopsis thaliana by the salt overly sensitive (SOS) pathway [J]. Journal of Biological Chemistry,2004, 279(1):207-215.
[21]Rodriguez-Rosales M.P., Galvez F.J., Huertas R., et al. Plant NHX Na+/H+antiporters [J]. Plant Signal Behavior,2009,4(4):265-276.
[22]Zhang HX, Hodson J.N., Williams J.P. et al. Engineering salt-tolerant Brassica plants: characterization of yield and seed oil quality in transgenic plants with increased vacuolar sodium accumulation [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(22):12832-12836.
[23]Barkla B.J., Vera-Estrella R., Camacho-Emiterio J., et al. Na+/H+exchange in the halophyte Mesembryanthemum crystallinum is associated with cellular sites of Na+storage [J]. Functional Plant Biology,2002,29(9):1017-1024.
[24]Ayala F., O'Leary J.W., Schumaker K.S. Increased vacuolar and plasma membrane H+-ATPase activities in Salicornia bigelovii Torr. in response to NaCl [J]. Journal of Experimental Botany, 1996,47(1):25-32.
[25]Qiu NW, Chen M, Guo JR, et al. Coordinate up-regulation of V-H+-ATPase and vacuolar Na+/H+ antiporter as a response to NaCl treatment in a C-3 halophyte Suaeda salsa [J]. Plant Science, 2007,172(6):1218-1225.
[26]Rus A., Yokoi S., Sharkhuu A., et al. AtHKTl is a salt tolerance determinant that controls Na+ entry into plant roots [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(24):14150-14155.
[27]Laurie S., Feeney K.A., Maathuis F.J., et al. A role for HKT1 in sodium uptake by wheat roots [J]. The Plant Journal,2002,32(2):139-149.
[28]Munns R., Tester M. Mechanisms of salinity tolerance [J]. Annual Review of Plant Biology, 2008,59:651-681.
[29]Flowers T., Colmer T. Salinity tolerance in halophytes [J]. New Phytologist,2008,179(4): 945-963.
[30]Delauney A.J., Verma D.P.S. Proline biosynthesis and osmoregulation in plants [J]. The Plant Journal,2002,4(2):215-223.
[31]Roosens N.H., Thu T.T., Iskandar H.M., et al. Isolation of the ornithine-δ-aminotransferase cDNA and effect of salt stress on its expression in Arabidopsis thaliana [J]. Plant Physiology, 1998,117(1):263-271.
[32]Armengaud P., Thiery L., Buhot N., et al. Transcriptional regulation of proline biosynthesis in Medicago truncatula reveals developmental and environmental specific features [J]. Physiologia Plantarum,2004,120(3):442-450.
[33]Tiirkan I., Demiral T. Recent developments in understanding salinity tolerance [J]. Environmental and Experimental Botany,2009,67(1):2-9.
[34]Waditee R., Bhuiyan N.H., Hirata E., et al. Metabolic engineering for betaine accumulation in microbes and plants [J]. Journal of Biology Chemistry,2007,282(47):34185-34193.
[35]Mahajan S., Tuteja N. Cold, salinity and drought stresses:an overview [J]. Archives of Biochemistry and Biophysics,2005,444(2):139-158.
[36]Waditee R., Bhuiyan M.N.H., Rai V., et al. Genes for direct methylation of glycine provide high levels of glycinebetaine and abiotic-stress tolerance in Synechococcus and Arabidopsis [J]. Proceedings of the National Academy of Sciences of the United States of America,2005,102(5): 1318-1323.
[37]Kishitani S., Takanami T., Suzuki M., et al. Compatibility of glycinebetaine in rice plants: evaluation using transgenic rice plants with a gene for peroxisomal betaine aldehyde dehydrogenase from barley [J]. Plant, Cell & Environment,2001,23(1):107-114.
[38]Bowler C., Slooten L., Vandenbranden S., et al. Manganese superoxide dismutase can reduce cellular damage mediated by oxygen radicals in transgenic plants [J]. The EMBO Journal,1991, 10(7):1723.
[39]Van Camp W., Capiau K., Van Montagu M., et al. Enhancement of oxidative stress tolerance in transgenic tobacco plants overproducing Fe-superoxide dismutase in chloroplasts [J]. Plant Physiology,1996,112(4):1703-1714.
[40]Badawi G.H., Kawano N., Yamauchi Y., et al. Over-expression of ascorbate peroxidase in tobacco chloroplasts enhances the tolerance to salt stress and water deficit [J]. Physiologia Plantarum,2004,121(2):231-238.
[41]Mohamed E.A., Iwaki T., Munir I., et al. Overexpression of bacterial catalase in tomato leaf chloroplasts enhances photooxidative stress tolerance [J]. Plant, Cell & Environment,2003, 26(12):2037-2046.
[42]Miller G, Suzuki N., Rizhsky L., et al. Double mutants deficient in cytosolic and thylakoid ascorbate peroxidase reveal a complex mode of interaction between reactive oxygen species, plant development, and response to abiotic stresses [J]. Plant Physiology,2007,144(4): 1777-1785.
[43]Rizhsky L., Hallak-Herr H., Van Breusegem F., et al. Double antisense plants lacking ascorbate peroxidase and catalase are less sensitive to oxidative stress than single antisense plants lacking ascorbate peroxidase or catalase [J]. The Plant Journal,2002,32(3):329-342.
[44]Shi H, Zhu JK. Regulation of expression of the vacuolar Na+/H+antiporter gene AtNHX1 by salt stress and abscisic acid [J]. Plant Molecular Biology,2002,50(3):543-550.
[45]Nakamura T., Liu Y, Hirata D., et al. Protein phosphatase type 2B (calcineurin)-mediated, FK506-sensitive regulation of intracellular ions in yeast is an important determinant for adaptation to high salt stress conditions [J]. The EMBO Journal,1993,12(11):4063.
[46]Shou H, Bordallo P., Fan JB., et al. Expression of an active tobacco mitogen-activated protein kinase kinase kinase enhances freezing tolerance in transgenic maize [J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(9):3298-3303.
[47]Wang Z, Gerstein M., Snyder M. RNA-Seq:a revolutionary tool for transcriptomics [J]. Nature Reviews Genetics,2009,10(1):57-63.
[48]Schena M., Shalon D., Davis R.W., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray [J]. Science,1995,270 (5235):467-470.
[49]Lipshutz R.J., Fodor S.P., Gingeras T.R. High density synthetic oligonucleotide arrays [J]. Nature Genetics,1999,21 (1):20-24.
[50]Schena M., Shalon D., Heller R. Parallel human genome analysis:microarray-based expression monitoring of 1000 genes [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(20):10614-10619.
[51]Bertone P., Stolc V., Royce T.E., et al. Global identification of human transcribed sequences with genome tiling arrays [J]. Science,2004,306(5705):2242-2246.
[52]Adams M.D., Kelley J.M., Gocayne J.D., et al. Complementary DNA sequencing:expressed sequence tags and human genome project [J]. Science,1991,252(5013):1651-1656.
[53]Velculescu V.E., Zhang L, Vogelstein B., et al. Serial analysis of gene expression [J]. Science, 1995,270(5235):484-487.
[54]Brenner S., Johnson M., Bridgham J., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J]. Nature biotechnology,2000,18(6): 630-634.
[55]Nagalakshmi U., Wang Z, Waern K., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing [J]. Science,2008,320(5881):1344-1349.
[56]Wilhelm B.T., Marguerat S., Watt S., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution [J]. Nature,2008,453(7199):1239-1243.
[57]Lister R., O'Malley R.C., Tonti-Filippini J., et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis [J]. Cell,2008,133(3):523-536.
[58]Mortazavi A., Williams B.A., McCue K., et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq [J]. Nature Methods,2008,5 (7):621-628.
[59]Wang ET, Sandberg R., Luo S, et al. Alternative isoform regulation in human tissue transcriptomes [J]. Nature,2008,456 (7221):470-476.
[60]Morin R.D., Bainbridge M., Fejes A., et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing [J]. Biotechniques,2008,45(1): 81-94.
[61]Mardis E.R. The impact of next-generation sequencing technology on genetics [J]. Trends in Genetics,2008,24(3):133.
[62]Brautigam A., Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research [J]. Plant Biology,2010,12(6):831-841.
[63]Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome [J]. Genome Research,2010,20(5):646-654.
[64]Wu J, Zhang Y, Zhang H, et al. Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology [J]. BMC Plant Biology, 2010,10(1):234.
[65]Li Y, Sun C, Luo HM, et al. Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX [J]. Acta pharmaceutica Sinica,2010,45(4):524-529.
[66]王曦,汪小我,王立坤,等.新一代高通量RNA测序数据的处理与分析[J].生物化学与生物物理进展,2010,37(8)：834-846.
[67]Kristiansson E., Asker N., Forlin L., et al. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing [J]. BMC genomics,2009,10(1):345.
[68]Mu Y, Ding F, Cui P, et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection [J]. BMC Genomics,2010,11(1):506.
[69]Wolf J.B., Bayer T., Haubold B., et al. Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow [J]. Molecular Ecology,2010,19(1):162-175.
[70]Ekblom R., Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms [J]. Heredity,2010,107(1):1-15.
[71]Trick M., Long Y, Meng J, et al. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing [J]. Plant Biotechnology Journal,2009,7(4):334-346.
[72]Novaes E., Drost D.R., Farmerie W.G., et al. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics,2008,9(1):312.
[73]Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants [J]. Annual Review Plant Biology.2006,57:19-53.
[74]Vaucheret H. Post-transcriptional small RNA pathways in plants:mechanisms and regulations [J]. Genes & Development,2006,20(7):759-771.
[75]Morin R.D., Aksay G., Dolgosheina E., et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa [J]. Genome Research,2008,18(4):571-584.
[76]Li T, Li H, Zhang YX, et al. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice(Oryza sativa L. ssp. indica) [J]. Nucleic Acids Research,2011,39(7):2821-2833.
[77]赵一之.鄂尔多斯高原维管植物[M].内蒙古大学出版社,2006,47.
[78]马毓泉.内蒙古植物志(第三卷)[M].呼和浩特：内蒙古人民出版社,1989,4(2)：519-522.
[79]杨持,王迎春,刘强,等.四合木保护生物学[M].北京：科学出版社,2002.
[80]傅立国.中国植物红皮书[M].北京：科学出版社,1992.
[81]中国科学院内蒙古宁夏综合考察队.内蒙古自治区与东北西部地区土壤地理[M].北京：科学出版社,1978,186-191.
[82]赵一之.长叶红沙(Reaumuria trigyna)植物区系地理分布研究[J].内蒙古大学学报,1996,27(3)：369-370.
[83]杨瑞丽.荒漠旱生小灌木劈裂生长的形态发生及其适应机制的比较研究[D].内蒙古大学硕士论文,2004.
[84]薛焱,王迎春.盐生植物长叶红砂泌盐特性的研究[J].中国沙漠,2008,28(3)：437-442.
[85]王镜岩,朱圣庚,徐长法.生物化学(第3版)[M].高等教育出版社,2002.
[86]张敏,王迎春.长叶红沙种子在萌发过程中细胞内营养物质动态研究[J]内蒙古大学学报(自然科学版),2006,37(5)：535-539.
[87]周健华.阿拉善荒漠区特有植物长叶红砂耐盐胁迫的生理响应.内蒙古大学硕士学位论文[D],2008.
[88]张颖娟,王玉山.濒危灌木长叶红砂遗传多样性的RAPD分析[J].生态学杂志,2008,27(2)：157-161.
[89]张颖娟,王玉山.濒危小灌木长叶红砂遗传多样性的ISSR研究[J].植物研究,2008,28(5)：568-573.
[90]张韬,王炜,安慧君,等.东阿拉善-西鄂尔多斯地区特有濒危植物种群斑块变化与优先保护级相关分析[J].干旱区资源与环境,2005,19(5)：179-184.
[91]史培军.地理环境演变研究的理论和实践,鄂尔多斯高原晚第四纪以来地理环境演变的研究[M].北京：科学出版社,1999.
[92]薛焱.阿拉善特有植物长叶红砂耐盐机理的研究[D].内蒙古大学博士学位论文,2008.
[93]张颖娟,郎秀平,李青丰.长叶红砂和红砂种子萌发对光照、温度和水分的响应[J].干旱区资源与环境,22(10)：167-171.
[94]周健华,王迎春,石松利.长叶红砂主要水分参数随季节和生境的变化[J].应用生态学报,20(11)：2624-2631.
[95]薛焱,王迎春,王同智.濒危植物长叶红砂适应盐胁迫的生理生化机制研究[J].西北植物学报,2012,32(1)：0136-0142.
[96]薛焱,王迎春,王同智.盐胁迫对濒危植物长叶红砂抗氧化系统的影响[J].中国沙漠,2012,32(6),1659-1673.
[97]Zhu JK. Plant salt tolerance [J]. Trends in Plant Science,2001,6(2):66-71.
[98]Zhang H, Han B, Wang T, et al. Mechanisms of plant salt response:insights from proteomics [J]. Journal of Proteome Research,2011,11(1):49-67.
[99]Rhoades J.D., Loveday J. Salinity in irrigated agriculture [J]. In American Society of Civil Engineers, Irrigation of Agricultural Crops,1990,30:1089-1142.
[100]Yeo A. Predicting the interaction between the effects of salinity and climate change on crop plants [J]. Scientia Horticulturae,1998,78(1):159-174.
[101]赵福庚,何龙飞,罗庆云.植物逆境生理生态学[M].北京：化学工业出版社,2004.
[102]Blumwald E., Aharon G.S., Apse M.P. Sodium transport in plant cells [J]. Biochimica et Biophysica Acta-Biomembranes-Including Reviews on Biomembranes,2000,1465(1):140-151.
[103]Conde A., Chaves M.M., Geros H. Membrane transport, sensing and signaling in plant adaptation to environmental stress [J]. Plant and Cell Physiology,2011,52(9):1583-1602.
[104]Breckle S.W. Salinity, halophytes and salt affected natural ecosystems [J]. Salinity: Environment Plants Molecules,2004:53-77.
[105]Alagna F., D'Agostino N., Torchia L., et al. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development [J]. BMC genomics,2009,10(1):399.
[106]Huang X, Madan A. CAP3:A DNA sequence assembly program [J]. Genome Research, 1999,9(9):868-877.
[107]Ashburner M., Ball C.A., Blake J.A., et al. Gene Ontology:tool for the unification of biology. Nature Genetics,2000,25(1):25.
[108]Conesa A., Gotz S., Garcia-Gomez J.M., et al. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research [J]. Bioinformatics,2005,21(18): 3674-3676.
[109]Ye J, Fang L, Zheng H, et al. WEGO:a web tool for plotting GO annotations [J]. Nucleic Acids Research,2006,34(suppl 2):W293-W297.
[110]Kanehisa M., Araki M., Goto S., et al. KEGG for linking genomes to life and the environment [J]. Nucleic Acids Research,2008,36(suppl 1):D480-D484.
[111]Iseli C., Jongeneel C.V., Bucher P. ESTScan:a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences [J]. Proceedings of International Conference on Intelligent Systems for Molecular Biology,1999:138-148.
[112]Hao DC, Ge GB, Xiao PG, et al. The first insight into the tissue specific Taxus transcriptome via Illumina second generation sequencing [J]. PLoS One,2011,6(6):e21220.
[113]Shi CY, Yang H, Wei CL, et al. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds [J]. BMC Genomics,2011,12(1):131.
[114]Audic S, Claverie J.M. The significance of digital gene expression profiles [J]. Genome Research,1997,7(10):986-995.
[115]Morozova O., Hirst M., Marra M.A. Applications of new sequencing technologies for transcriptome analysis [J]. Annual Review of Genomics and Human Genetics,2009,10: 135-151.
[116]Blumwald E. Sodium transport and salt tolerance in plants [J]. Current Opinion Cell Biology, 2000,12(4):431-434.
[117]Chinnusamy V, Zhu J, Zhu JK. Salt stress signaling and mechanisms of plant salt tolerance [J]. Genetic Engineering,2006,27:141-177.
[118]Niu XM, Bressan R.A., Hasegawa P.M., et al. Ion homeostasis in NaCl stress environments [J]. Plant Physiology,1995,109(3):735-742.
[119]Chen S, Polle A. Salinity tolerance of Populus [J]. Plant Biology,2010,12(2):317-333.
[120]Sun J, Dai SX, Wang RG, et al. Calcium mediates root K+/Na+homeostasis in poplar species differing in salt tolerance [J]. Tree Physiology,2009,29(9):1175-1186.
[121]Bassil E., Tajima H., Liang YC, et al. The Arabidopsis Na+/H+antiporters NHX1 and NHX2 control vacuolar pH and K+homeostasis to regulate growth, flower development, and reproduction [J]. The Plant Cell Online,2011,23(9):3482-3497.
[122]Wu YX, Ding N, Zhao X, et al. Molecular characterization of PeSOS1:the putative Na+/H+ antiporter of Populus euphratica [J]. Plant Molecular Biology,2007,65(1):1-11.
[123]Taji T., Seki M., Satou M., et al. Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte cress using Arabidopsis microarray [J]. Plant Physiology,2004,135(3):1697-1709.
[124]Ottow E.A., Polle A., Brosche M., et al. Molecular characterization of PeNhaD1:the first member of the NhaD Na+/H+antiporter family of plant origin [J]. Plant Molecular Biology,2005, 58(1):75-88.
[125]Mittler R. Oxidative stress, antioxidants and stress tolerance [J]. Trends in Plant Science, 2002,7(9):405-410.
[126]Miller G., Shulaev V, Mittler R. Reactive oxygen signaling and abiotic stress [J]. Physiologia Plantarum,2008,133(3):481-489.
[127]Dixon D.P., Lapthorn A., Edwards R. Plant glutathione transferases [J]. Genome Biology, 2002,3(3):1-10.
[128]Kilili K.G, Atanassova N., Vardanyan A., et al. Differential roles of Tau class glutathione S-transferases in oxidative stress [J]. Journal of Biological Chemistry,2004,279(23): 24540-24551.
[129]Pang QY, Chen SX, Dai SJ, et al. Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila [J]. Journal of Proteome Research,2010,9(5):2584-2599.
[130]Chen FG, Zhang S, Jiang H, et al. Comparative proteomics analysis of salt response reveals sex-related photosynthetic inhibition by salinity in Populus cathayana cuttings [J]. Journal of Proteome Research,2011,10(9):3944-3958.
[131]Liu GQ, Li WS, Zheng PH, et al. Transcriptomic analysis of'Suli'pear(Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq [J]. BMC Genomics,2012,13(1): 700.
[132]Zhou YJ, Gao F, Liu R, et al. De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus [J]. BMC Genomics,2012,13(1):266.
[133]Dang ZH, Zheng LL, Wang J, et al. Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna [J]. BMC Genomics,2013,14(1):29.
[134]Gahlan P., Singh H.R., Shankar R., et al. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments [J]. BMC Genomics,2012,13(1):126.
[135]Sung YJ, Denman RB. Use of two reverse transcriptases eliminates false-positive results in differential display [J]. Biotechniques,1997,23(3):462-464,466,468.
[136]Bhattacharjee A., Rutherford M.S., Abrahamsen M.S., et al. Refinements in re-amplification and cloning of DDRT-PCR products [J]. Biotechniques,1997,22(6):1048-1051.
[137]Tautz D., Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes [J]. Nucleic Acids Research,1984,12(10):4127-4138.
[138]Lagercrantz U., Ellegren H., Andersson L. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates [J]. Nucleic Acids Research,1993, 21(5):1111-1115.
[139]Rafalski J.A., Tingey S.V. Genetic diagnostics in plant breeding:RAPDs, microsatellites and machines [J]. Trends in Genetics,1993,9(8):275-280.
[140]李淑娴,张新叶,王英亚,等.按树EST序列中微卫星含量及相关特征[J].植物学报,2010,45(3)：363-371.
[141]王丽鸳,姜燕华,段云裳,等.茶树EST-SSRs分布特征及引物开发[J].植物遗传资源学报,2009,10(4)：511-516.
[142]王丽鸳,刘本英,姜燕华,等.用SSR分子标记研究茶组植物种间亲缘进化关系[J].茶叶科学,2009,29(5)：341-346.
[143]Schlotterer C., Tautz D. Slippage synthesis of simple sequence DNA [J]. Nucleic Acids Research,1992,20(2):211-215.
[144]Aerts J.A., Jungerius B.J., Groenen M.A. POSA:perl objects for DNA sequencing data analysis [J]. BMC genomics,2004,5(1):60.
[145]徐静,吕炳建,张昊,等.电子基因表达谱分析平台的建立及其应用[J].浙江大学学报工学版,2006,40(2)：186-191.
[146]周猛,童春发,施季森.充分利用Bioperl加速生物信息学的研究[J].生物信息学,2006,6(1)：43-45.
[2]Ashraf M., Wu DL. Breeding for salinity tolerance in plants [J]. Critical Reviews in Plant Sciences,1994,13(1):17-42.
[3]赵可夫,冯立田.中国盐生植物资源[M].1998,北京：科学出版社.
[4]王宝山,赵可夫,邹琦.作物耐盐机理研究进展及提高作物抗盐性的对策[J].植物学通报,1997,14(1)：25-30.
[5]Zhu JK. Salt and drought stress signal transduction in plants [J]. Annual Review of Plant Biology, 2002,53:247.
[6]Zhu JK. Regulation of ion homeostasis under salt stress [J]. Current Opinion in Plant Biology, 2003,6(5):441-445.
[7]Abogadallah GM. Antioxidative defense under salt stress [J]. Plant Signal Behavior,2010,5(4): 369-374.
[8]Vinocur B., Altman A. Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations [J]. Current Opinion in Biotechnology,2005,16(2):123-132.
[9]Tuteja N. Mechanisms of high salinity tolerance in plants [J]. Methods in Nnzymology,2007, 428:419.
[10]Flowers T., Troke P., Yeo A. The mechanism of salt tolerance in halophytes [J]. Annual Review of Plant Physiology,1977,28(1):89-121.
[11]Greenway H., Munns R. Mechanisms of salt tolerance in nonhalophytes [J]. Annual Review of Plant Physiology,1980,31(1):149-190.
[12]Yamaguchi T., Blumwald E. Developing salt-tolerant crop plants:challenges and opportunities [J]. Trends in Plant Science,2005,10(12):615-620.
[13]Gaxiola R.A., Li J, Undurraga S., et al. Drought-and salt-tolerant plants result from overexpression of the AVP1 H+-pump [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(20):11444-11449.
[14]Pasapula V., Shen G, Kuppu S., et al. Expression of an Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) in cotton improves drought-and salt tolerance and increases fiber yield in the field conditions [J]. Plant Biotechnology Journal 2011,9(1):88-99.
[15]Li Z, Baldwin C.M., Hu Q, et al. Heterologous expression of Arabidopsis H+-pyrophosphatase enhances salt tolerance in transgenic creeping bent grass (Agrostis stolonifera L.) [J]. Plant, Cell & Environment,2009,33(2):272-289.
[16]Xue ZY, Zhi DY, Xue GP, et al. Enhanced salt tolerance of transgenic wheat (Tritivum aestivum L.) expressing a vacuolar Na+/H+antiporter gene with improved grain yields in saline soils in the field and a reduced level of leaf Na+[J]. Plant Science,2004,167,849-859.
[17]Yin XY, Yang AF, Zhang KW, et al. Production and analysis of transgenic maize with improved salt tolerance by the introduction of AtNHXl gene [J]. Acta Botanica Sinica,2004,46(7): 854-861.
[18]Zhang HX, Blumwald E. Transgenic salt-tolerant tomato plants accumulate salt in foliage but not in fruit [J]. Nature Biotechnology,2001,19(8),765-768.
[19]Wu L.Q., Fan Z.M., Qu L.J. et al. Overexpression of the bacterial nhaA gene in rice enhances salt and drought tolerance [J]. Plant Science,2005,168(2):297-302.
[20]Qiu QS, Guo Y, Quintero F.J., et al. Regulation of vacuolar Na+/H+exchange in Arabidopsis thaliana by the salt overly sensitive (SOS) pathway [J]. Journal of Biological Chemistry,2004, 279(1):207-215.
[21]Rodriguez-Rosales M.P., Galvez F.J., Huertas R., et al. Plant NHX Na+/H+antiporters [J]. Plant Signal Behavior,2009,4(4):265-276.
[22]Zhang HX, Hodson J.N., Williams J.P. et al. Engineering salt-tolerant Brassica plants: characterization of yield and seed oil quality in transgenic plants with increased vacuolar sodium accumulation [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(22):12832-12836.
[23]Barkla B.J., Vera-Estrella R., Camacho-Emiterio J., et al. Na+/H+exchange in the halophyte Mesembryanthemum crystallinum is associated with cellular sites of Na+storage [J]. Functional Plant Biology,2002,29(9):1017-1024.
[24]Ayala F., O'Leary J.W., Schumaker K.S. Increased vacuolar and plasma membrane H+-ATPase activities in Salicornia bigelovii Torr. in response to NaCl [J]. Journal of Experimental Botany, 1996,47(1):25-32.
[25]Qiu NW, Chen M, Guo JR, et al. Coordinate up-regulation of V-H+-ATPase and vacuolar Na+/H+ antiporter as a response to NaCl treatment in a C-3 halophyte Suaeda salsa [J]. Plant Science, 2007,172(6):1218-1225.
[26]Rus A., Yokoi S., Sharkhuu A., et al. AtHKTl is a salt tolerance determinant that controls Na+ entry into plant roots [J]. Proceedings of the National Academy of Sciences of the United States of America,2001,98(24):14150-14155.
[27]Laurie S., Feeney K.A., Maathuis F.J., et al. A role for HKT1 in sodium uptake by wheat roots [J]. The Plant Journal,2002,32(2):139-149.
[28]Munns R., Tester M. Mechanisms of salinity tolerance [J]. Annual Review of Plant Biology, 2008,59:651-681.
[29]Flowers T., Colmer T. Salinity tolerance in halophytes [J]. New Phytologist,2008,179(4): 945-963.
[30]Delauney A.J., Verma D.P.S. Proline biosynthesis and osmoregulation in plants [J]. The Plant Journal,2002,4(2):215-223.
[31]Roosens N.H., Thu T.T., Iskandar H.M., et al. Isolation of the ornithine-δ-aminotransferase cDNA and effect of salt stress on its expression in Arabidopsis thaliana [J]. Plant Physiology, 1998,117(1):263-271.
[32]Armengaud P., Thiery L., Buhot N., et al. Transcriptional regulation of proline biosynthesis in Medicago truncatula reveals developmental and environmental specific features [J]. Physiologia Plantarum,2004,120(3):442-450.
[33]Tiirkan I., Demiral T. Recent developments in understanding salinity tolerance [J]. Environmental and Experimental Botany,2009,67(1):2-9.
[34]Waditee R., Bhuiyan N.H., Hirata E., et al. Metabolic engineering for betaine accumulation in microbes and plants [J]. Journal of Biology Chemistry,2007,282(47):34185-34193.
[35]Mahajan S., Tuteja N. Cold, salinity and drought stresses:an overview [J]. Archives of Biochemistry and Biophysics,2005,444(2):139-158.
[36]Waditee R., Bhuiyan M.N.H., Rai V., et al. Genes for direct methylation of glycine provide high levels of glycinebetaine and abiotic-stress tolerance in Synechococcus and Arabidopsis [J]. Proceedings of the National Academy of Sciences of the United States of America,2005,102(5): 1318-1323.
[37]Kishitani S., Takanami T., Suzuki M., et al. Compatibility of glycinebetaine in rice plants: evaluation using transgenic rice plants with a gene for peroxisomal betaine aldehyde dehydrogenase from barley [J]. Plant, Cell & Environment,2001,23(1):107-114.
[38]Bowler C., Slooten L., Vandenbranden S., et al. Manganese superoxide dismutase can reduce cellular damage mediated by oxygen radicals in transgenic plants [J]. The EMBO Journal,1991, 10(7):1723.
[39]Van Camp W., Capiau K., Van Montagu M., et al. Enhancement of oxidative stress tolerance in transgenic tobacco plants overproducing Fe-superoxide dismutase in chloroplasts [J]. Plant Physiology,1996,112(4):1703-1714.
[40]Badawi G.H., Kawano N., Yamauchi Y., et al. Over-expression of ascorbate peroxidase in tobacco chloroplasts enhances the tolerance to salt stress and water deficit [J]. Physiologia Plantarum,2004,121(2):231-238.
[41]Mohamed E.A., Iwaki T., Munir I., et al. Overexpression of bacterial catalase in tomato leaf chloroplasts enhances photooxidative stress tolerance [J]. Plant, Cell & Environment,2003, 26(12):2037-2046.
[42]Miller G, Suzuki N., Rizhsky L., et al. Double mutants deficient in cytosolic and thylakoid ascorbate peroxidase reveal a complex mode of interaction between reactive oxygen species, plant development, and response to abiotic stresses [J]. Plant Physiology,2007,144(4): 1777-1785.
[43]Rizhsky L., Hallak-Herr H., Van Breusegem F., et al. Double antisense plants lacking ascorbate peroxidase and catalase are less sensitive to oxidative stress than single antisense plants lacking ascorbate peroxidase or catalase [J]. The Plant Journal,2002,32(3):329-342.
[44]Shi H, Zhu JK. Regulation of expression of the vacuolar Na+/H+antiporter gene AtNHX1 by salt stress and abscisic acid [J]. Plant Molecular Biology,2002,50(3):543-550.
[45]Nakamura T., Liu Y, Hirata D., et al. Protein phosphatase type 2B (calcineurin)-mediated, FK506-sensitive regulation of intracellular ions in yeast is an important determinant for adaptation to high salt stress conditions [J]. The EMBO Journal,1993,12(11):4063.
[46]Shou H, Bordallo P., Fan JB., et al. Expression of an active tobacco mitogen-activated protein kinase kinase kinase enhances freezing tolerance in transgenic maize [J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(9):3298-3303.
[47]Wang Z, Gerstein M., Snyder M. RNA-Seq:a revolutionary tool for transcriptomics [J]. Nature Reviews Genetics,2009,10(1):57-63.
[48]Schena M., Shalon D., Davis R.W., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray [J]. Science,1995,270 (5235):467-470.
[49]Lipshutz R.J., Fodor S.P., Gingeras T.R. High density synthetic oligonucleotide arrays [J]. Nature Genetics,1999,21 (1):20-24.
[50]Schena M., Shalon D., Heller R. Parallel human genome analysis:microarray-based expression monitoring of 1000 genes [J]. Proceedings of the National Academy of Sciences of the United States of America,1996,93(20):10614-10619.
[51]Bertone P., Stolc V., Royce T.E., et al. Global identification of human transcribed sequences with genome tiling arrays [J]. Science,2004,306(5705):2242-2246.
[52]Adams M.D., Kelley J.M., Gocayne J.D., et al. Complementary DNA sequencing:expressed sequence tags and human genome project [J]. Science,1991,252(5013):1651-1656.
[53]Velculescu V.E., Zhang L, Vogelstein B., et al. Serial analysis of gene expression [J]. Science, 1995,270(5235):484-487.
[54]Brenner S., Johnson M., Bridgham J., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J]. Nature biotechnology,2000,18(6): 630-634.
[55]Nagalakshmi U., Wang Z, Waern K., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing [J]. Science,2008,320(5881):1344-1349.
[56]Wilhelm B.T., Marguerat S., Watt S., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution [J]. Nature,2008,453(7199):1239-1243.
[57]Lister R., O'Malley R.C., Tonti-Filippini J., et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis [J]. Cell,2008,133(3):523-536.
[58]Mortazavi A., Williams B.A., McCue K., et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq [J]. Nature Methods,2008,5 (7):621-628.
[59]Wang ET, Sandberg R., Luo S, et al. Alternative isoform regulation in human tissue transcriptomes [J]. Nature,2008,456 (7221):470-476.
[60]Morin R.D., Bainbridge M., Fejes A., et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing [J]. Biotechniques,2008,45(1): 81-94.
[61]Mardis E.R. The impact of next-generation sequencing technology on genetics [J]. Trends in Genetics,2008,24(3):133.
[62]Brautigam A., Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research [J]. Plant Biology,2010,12(6):831-841.
[63]Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome [J]. Genome Research,2010,20(5):646-654.
[64]Wu J, Zhang Y, Zhang H, et al. Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology [J]. BMC Plant Biology, 2010,10(1):234.
[65]Li Y, Sun C, Luo HM, et al. Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX [J]. Acta pharmaceutica Sinica,2010,45(4):524-529.
[66]王曦,汪小我,王立坤,等.新一代高通量RNA测序数据的处理与分析[J].生物化学与生物物理进展,2010,37(8)：834-846.
[67]Kristiansson E., Asker N., Forlin L., et al. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing [J]. BMC genomics,2009,10(1):345.
[68]Mu Y, Ding F, Cui P, et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection [J]. BMC Genomics,2010,11(1):506.
[69]Wolf J.B., Bayer T., Haubold B., et al. Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow [J]. Molecular Ecology,2010,19(1):162-175.
[70]Ekblom R., Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms [J]. Heredity,2010,107(1):1-15.
[71]Trick M., Long Y, Meng J, et al. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing [J]. Plant Biotechnology Journal,2009,7(4):334-346.
[72]Novaes E., Drost D.R., Farmerie W.G., et al. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics,2008,9(1):312.
[73]Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants [J]. Annual Review Plant Biology.2006,57:19-53.
[74]Vaucheret H. Post-transcriptional small RNA pathways in plants:mechanisms and regulations [J]. Genes & Development,2006,20(7):759-771.
[75]Morin R.D., Aksay G., Dolgosheina E., et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa [J]. Genome Research,2008,18(4):571-584.
[76]Li T, Li H, Zhang YX, et al. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice(Oryza sativa L. ssp. indica) [J]. Nucleic Acids Research,2011,39(7):2821-2833.
[77]赵一之.鄂尔多斯高原维管植物[M].内蒙古大学出版社,2006,47.
[78]马毓泉.内蒙古植物志(第三卷)[M].呼和浩特：内蒙古人民出版社,1989,4(2)：519-522.
[79]杨持,王迎春,刘强,等.四合木保护生物学[M].北京：科学出版社,2002.
[80]傅立国.中国植物红皮书[M].北京：科学出版社,1992.
[81]中国科学院内蒙古宁夏综合考察队.内蒙古自治区与东北西部地区土壤地理[M].北京：科学出版社,1978,186-191.
[82]赵一之.长叶红沙(Reaumuria trigyna)植物区系地理分布研究[J].内蒙古大学学报,1996,27(3)：369-370.
[83]杨瑞丽.荒漠旱生小灌木劈裂生长的形态发生及其适应机制的比较研究[D].内蒙古大学硕士论文,2004.
[84]薛焱,王迎春.盐生植物长叶红砂泌盐特性的研究[J].中国沙漠,2008,28(3)：437-442.
[85]王镜岩,朱圣庚,徐长法.生物化学(第3版)[M].高等教育出版社,2002.
[86]张敏,王迎春.长叶红沙种子在萌发过程中细胞内营养物质动态研究[J]内蒙古大学学报(自然科学版),2006,37(5)：535-539.
[87]周健华.阿拉善荒漠区特有植物长叶红砂耐盐胁迫的生理响应.内蒙古大学硕士学位论文[D],2008.
[88]张颖娟,王玉山.濒危灌木长叶红砂遗传多样性的RAPD分析[J].生态学杂志,2008,27(2)：157-161.
[89]张颖娟,王玉山.濒危小灌木长叶红砂遗传多样性的ISSR研究[J].植物研究,2008,28(5)：568-573.
[90]张韬,王炜,安慧君,等.东阿拉善-西鄂尔多斯地区特有濒危植物种群斑块变化与优先保护级相关分析[J].干旱区资源与环境,2005,19(5)：179-184.
[91]史培军.地理环境演变研究的理论和实践,鄂尔多斯高原晚第四纪以来地理环境演变的研究[M].北京：科学出版社,1999.
[92]薛焱.阿拉善特有植物长叶红砂耐盐机理的研究[D].内蒙古大学博士学位论文,2008.
[93]张颖娟,郎秀平,李青丰.长叶红砂和红砂种子萌发对光照、温度和水分的响应[J].干旱区资源与环境,22(10)：167-171.
[94]周健华,王迎春,石松利.长叶红砂主要水分参数随季节和生境的变化[J].应用生态学报,20(11)：2624-2631.
[95]薛焱,王迎春,王同智.濒危植物长叶红砂适应盐胁迫的生理生化机制研究[J].西北植物学报,2012,32(1)：0136-0142.
[96]薛焱,王迎春,王同智.盐胁迫对濒危植物长叶红砂抗氧化系统的影响[J].中国沙漠,2012,32(6),1659-1673.
[97]Zhu JK. Plant salt tolerance [J]. Trends in Plant Science,2001,6(2):66-71.
[98]Zhang H, Han B, Wang T, et al. Mechanisms of plant salt response:insights from proteomics [J]. Journal of Proteome Research,2011,11(1):49-67.
[99]Rhoades J.D., Loveday J. Salinity in irrigated agriculture [J]. In American Society of Civil Engineers, Irrigation of Agricultural Crops,1990,30:1089-1142.
[100]Yeo A. Predicting the interaction between the effects of salinity and climate change on crop plants [J]. Scientia Horticulturae,1998,78(1):159-174.
[101]赵福庚,何龙飞,罗庆云.植物逆境生理生态学[M].北京：化学工业出版社,2004.
[102]Blumwald E., Aharon G.S., Apse M.P. Sodium transport in plant cells [J]. Biochimica et Biophysica Acta-Biomembranes-Including Reviews on Biomembranes,2000,1465(1):140-151.
[103]Conde A., Chaves M.M., Geros H. Membrane transport, sensing and signaling in plant adaptation to environmental stress [J]. Plant and Cell Physiology,2011,52(9):1583-1602.
[104]Breckle S.W. Salinity, halophytes and salt affected natural ecosystems [J]. Salinity: Environment Plants Molecules,2004:53-77.
[105]Alagna F., D'Agostino N., Torchia L., et al. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development [J]. BMC genomics,2009,10(1):399.
[106]Huang X, Madan A. CAP3:A DNA sequence assembly program [J]. Genome Research, 1999,9(9):868-877.
[107]Ashburner M., Ball C.A., Blake J.A., et al. Gene Ontology:tool for the unification of biology. Nature Genetics,2000,25(1):25.
[108]Conesa A., Gotz S., Garcia-Gomez J.M., et al. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research [J]. Bioinformatics,2005,21(18): 3674-3676.
[109]Ye J, Fang L, Zheng H, et al. WEGO:a web tool for plotting GO annotations [J]. Nucleic Acids Research,2006,34(suppl 2):W293-W297.
[110]Kanehisa M., Araki M., Goto S., et al. KEGG for linking genomes to life and the environment [J]. Nucleic Acids Research,2008,36(suppl 1):D480-D484.
[111]Iseli C., Jongeneel C.V., Bucher P. ESTScan:a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences [J]. Proceedings of International Conference on Intelligent Systems for Molecular Biology,1999:138-148.
[112]Hao DC, Ge GB, Xiao PG, et al. The first insight into the tissue specific Taxus transcriptome via Illumina second generation sequencing [J]. PLoS One,2011,6(6):e21220.
[113]Shi CY, Yang H, Wei CL, et al. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds [J]. BMC Genomics,2011,12(1):131.
[114]Audic S, Claverie J.M. The significance of digital gene expression profiles [J]. Genome Research,1997,7(10):986-995.
[115]Morozova O., Hirst M., Marra M.A. Applications of new sequencing technologies for transcriptome analysis [J]. Annual Review of Genomics and Human Genetics,2009,10: 135-151.
[116]Blumwald E. Sodium transport and salt tolerance in plants [J]. Current Opinion Cell Biology, 2000,12(4):431-434.
[117]Chinnusamy V, Zhu J, Zhu JK. Salt stress signaling and mechanisms of plant salt tolerance [J]. Genetic Engineering,2006,27:141-177.
[118]Niu XM, Bressan R.A., Hasegawa P.M., et al. Ion homeostasis in NaCl stress environments [J]. Plant Physiology,1995,109(3):735-742.
[119]Chen S, Polle A. Salinity tolerance of Populus [J]. Plant Biology,2010,12(2):317-333.
[120]Sun J, Dai SX, Wang RG, et al. Calcium mediates root K+/Na+homeostasis in poplar species differing in salt tolerance [J]. Tree Physiology,2009,29(9):1175-1186.
[121]Bassil E., Tajima H., Liang YC, et al. The Arabidopsis Na+/H+antiporters NHX1 and NHX2 control vacuolar pH and K+homeostasis to regulate growth, flower development, and reproduction [J]. The Plant Cell Online,2011,23(9):3482-3497.
[122]Wu YX, Ding N, Zhao X, et al. Molecular characterization of PeSOS1:the putative Na+/H+ antiporter of Populus euphratica [J]. Plant Molecular Biology,2007,65(1):1-11.
[123]Taji T., Seki M., Satou M., et al. Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte cress using Arabidopsis microarray [J]. Plant Physiology,2004,135(3):1697-1709.
[124]Ottow E.A., Polle A., Brosche M., et al. Molecular characterization of PeNhaD1:the first member of the NhaD Na+/H+antiporter family of plant origin [J]. Plant Molecular Biology,2005, 58(1):75-88.
[125]Mittler R. Oxidative stress, antioxidants and stress tolerance [J]. Trends in Plant Science, 2002,7(9):405-410.
[126]Miller G., Shulaev V, Mittler R. Reactive oxygen signaling and abiotic stress [J]. Physiologia Plantarum,2008,133(3):481-489.
[127]Dixon D.P., Lapthorn A., Edwards R. Plant glutathione transferases [J]. Genome Biology, 2002,3(3):1-10.
[128]Kilili K.G, Atanassova N., Vardanyan A., et al. Differential roles of Tau class glutathione S-transferases in oxidative stress [J]. Journal of Biological Chemistry,2004,279(23): 24540-24551.
[129]Pang QY, Chen SX, Dai SJ, et al. Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila [J]. Journal of Proteome Research,2010,9(5):2584-2599.
[130]Chen FG, Zhang S, Jiang H, et al. Comparative proteomics analysis of salt response reveals sex-related photosynthetic inhibition by salinity in Populus cathayana cuttings [J]. Journal of Proteome Research,2011,10(9):3944-3958.
[131]Liu GQ, Li WS, Zheng PH, et al. Transcriptomic analysis of'Suli'pear(Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq [J]. BMC Genomics,2012,13(1): 700.
[132]Zhou YJ, Gao F, Liu R, et al. De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus [J]. BMC Genomics,2012,13(1):266.
[133]Dang ZH, Zheng LL, Wang J, et al. Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna [J]. BMC Genomics,2013,14(1):29.
[134]Gahlan P., Singh H.R., Shankar R., et al. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments [J]. BMC Genomics,2012,13(1):126.
[135]Sung YJ, Denman RB. Use of two reverse transcriptases eliminates false-positive results in differential display [J]. Biotechniques,1997,23(3):462-464,466,468.
[136]Bhattacharjee A., Rutherford M.S., Abrahamsen M.S., et al. Refinements in re-amplification and cloning of DDRT-PCR products [J]. Biotechniques,1997,22(6):1048-1051.
[137]Tautz D., Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes [J]. Nucleic Acids Research,1984,12(10):4127-4138.
[138]Lagercrantz U., Ellegren H., Andersson L. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates [J]. Nucleic Acids Research,1993, 21(5):1111-1115.
[139]Rafalski J.A., Tingey S.V. Genetic diagnostics in plant breeding:RAPDs, microsatellites and machines [J]. Trends in Genetics,1993,9(8):275-280.
[140]李淑娴,张新叶,王英亚,等.按树EST序列中微卫星含量及相关特征[J].植物学报,2010,45(3)：363-371.
[141]王丽鸳,姜燕华,段云裳,等.茶树EST-SSRs分布特征及引物开发[J].植物遗传资源学报,2009,10(4)：511-516.
[142]王丽鸳,刘本英,姜燕华,等.用SSR分子标记研究茶组植物种间亲缘进化关系[J].茶叶科学,2009,29(5)：341-346.
[143]Schlotterer C., Tautz D. Slippage synthesis of simple sequence DNA [J]. Nucleic Acids Research,1992,20(2):211-215.
[144]Aerts J.A., Jungerius B.J., Groenen M.A. POSA:perl objects for DNA sequencing data analysis [J]. BMC genomics,2004,5(1):60.
[145]徐静,吕炳建,张昊,等.电子基因表达谱分析平台的建立及其应用[J].浙江大学学报工学版,2006,40(2)：186-191.
[146]周猛,童春发,施季森.充分利用Bioperl加速生物信息学的研究[J].生物信息学,2006,6(1)：43-45.
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