稻属分蘖控制基因（MOC1）直向同源区的比较序列分析
|
摘要
分蘖现象是水稻、小麦等禾本科作物在生长发育过程中的一种特殊的分枝特性,它直接决定水稻、小麦等的穗数及其产量,而且与创建理想株型密切相关。稻属中广泛分布在热带、亚热带地区的野生稻具有丰富的遗传多样性,以及许多优异的栽培稻中已灭绝了的基因,是栽培稻产量、品质、抗性以及其它农艺性状改良的重要的基因库。随着粳稻日本晴(Oryza sativa L. ssp. Japonica cv. Nipponbare)和籼稻93-11(Oryza sativa L. ssp. Indica cv. 93-11)基因组计划的完成及测序成本的日趋下降,开展核苷酸水平的比较基因组学研究变得越来越现实。因此,为有效的利用稻属野生资源提供一定理论和技术支撑,本研究在序列水平采用比较基因组学的方法,并结合生物信息学技术,对整个稻属各基因组类型植物中的MONOCULM1(MOC1)直向同源区进行了比较分析,得出如下重要结论。
比较基因组学方法是一个提高基因注释准确性的强有力的手段。通过RT-PCR试验及随后测序方法发现了NCBI对粳稻日本晴的一个基因注释有误,NCBI的注释多出了一段长15个核苷酸的序列。
稻属中多数直向同源基因是很保守的,且多外显子基因的外显子-内含子结构也很保守,基因种类及其排列顺序也都表现出了较高的保守性。此外,还发现了一些个别基因组特有的基因。在本研究所有的BAC中存在直向同源基因的是MOC1和探针42DP1006所来自的基因。其它的基因只是在一些BAC中有直向同源基因,而另一些BAC中则没有,这主要是由于某些基因组类型的野生稻BAC较小,序列不够长所致,同时某些MOC1同源BAC中(尤其是四倍体)有较多的重复序列导致基因密度很低,也是该同源区所共有的直向同源基因少的重要原因。
稻属中各MOC1同源区平均每个基因的外显子数目相差不大。AA组基因密度较高,四倍体基因组中(除CCDD基因组外)两个MOC1同源BAC均表现出一个基因密度较高,而另一个基因密度很低的现象。
发现了一例整个基因序列完全从头形成的新基因产生过程。通过序列比对发现,从稻属植物中亲缘关系较远的GG基因组,开始只有一段长度有限的保守的DNA序列,到CC组保守序列逐渐变长,到BB组和AA组就形成了一个新基因,即日本晴MOC1 PAC上的第13号基因及其在AA组和BB组中的直向同源基因,该基因有全长cDNA(AK062635)支持(100%)。
在多个稻属物种中找到了基因组加倍或基因加倍后复制基因去功能化的分子证据。稻属四倍体物种中除CCDD基因组的O. alta外,探针42DP1006的两个同源基因中均有一个在多次重复RT-PCR试验中均未扩增出任何产物。GG基因组的O. granulata中,该同源基因发生了串联复制,形成前后两个同源拷贝并被逆转座子插入而分开,其中上游的拷贝在多次重复RT-PCR试验中也均未扩增出任何产物。因此,推测加倍后的复制基因发生了去功能化。
发现了一个在基因密度、基因表达上比较特殊的四倍体O. alta。在本研究所涉及的MOC1同源区内,CCDD基因组O. alta中的两套遗传物质都有较高的基因密度(CC,9.8kb/基因;DD,10.1kb/基因),且探针42DP1006的直向同源基因对都保持了一定表达能力。此外,O. alta中的日本晴MOC1 PAC上第6号基因的一个同源基因虽被长约4kb的一个逆转座子插入到第3个内含子中但并没有影响该同源基因的表达,而且该四倍体的另一个同源基因在表达上也是正常的。
稻属植物基因组膨胀的主要动力是转座子和逆转座子扩增。研究发现稻属植物中基因组较小的AA组(350Mb~448Mb)和FF组(338Mb)具有较多的MITE(AA,16个~21个;FF,30个)和Tc1-IS630-Pogo(AA,18个~34个;FF,32个);而其它基因组较大(除BB组423Mb外,均在650Mb以上)的则这两种DNA型转座子较少。从LTR型逆转座子的数量上来看,情况正好相反,即AA组、FF组较少,而其它基因组类型则较多。从转座子和逆转座子累计长度占BAC序列长度的比重上看,也表现出了较大基因组类型中逆转座子所占比重较大,且转座子所占比重也不低的趋势。这暗示,稻属植物膨胀主要是由于转座子和逆转座子扩增造成的,而且有研究表明这可能是生物界基因组膨胀的普遍规律。
用邻接法(Neighbor-Joining)、最大简约法(Maximum Parsimony)、最小进化法(Minimum Evolution)等构建的比较一致的MOC1基因进化树表明,稻属植物中与AA基因组亲缘关系较近的是BB组(包括四倍体中的BB组),其次是CC组(包括四倍体中的CC组),而后是DD组和EE组,HHJJ、HHKK、GG、FF等组与AA组间亲缘关系较远。
Tillering is the ramifying trait emerging in the period of growth of some grass species e.g. rice, wheat, et al.. Tillering that is close correlate with the creating of ideal plant shape is the main deciding factor of spike numbers and the consequent yield of rice, wheat, et al. The wild rice species distributed in the Torrid Zone and sub-Torrid Zone possess abundant genetic diversity and excellent genes that do not exist in cultivated rice varieties. So, the wild rice species become important gene pools for improving yield, grain quality, stress resistance, and other agronomic traits of cultivated rice varieties. Along with the completion of genome project of Oryza sativa L. ssp. Japonica cv. Nipponbare and Oryza sativa L. ssp. Indica cv. 93-11 and the sequencing cost dropping more and more, to do some work about comparative genomics at DNA sequence level become more and more realizable. So, in order to give some theoretical and technological support for the wild rice resources utilizing effectively, the comparative analysis among MONOCULM1 (MOC1) orthologous regions in Oryza genus has been done by employing the methods of comparative genomics at DNA sequence level and bioinformatics. The results are depicted as follows.
The comparative genomics is a strongly method to improving the veracity of gene annotation. One gene annotation error in NCBI was discovered through RT-PCR and subsequently sequencing. 15bp nucleotides in the coding sequence of this gene annotated in NCBI is excessive than the reality of this gene.
The majority of orthologous genes and the intron-exon structures of these genes in Oryza genus are much conserved and the gene contents and order is also. Some genome specific genes were found. The orthologous genes existed all over in the BACs sequenced in this research are MOC1 and the gene that probe 42DP1006 is come from on Japonica MOC1 PAC. Other genes on MOC1 PAC except the two mentioned above can be found their orthologous genes from several BACs only. The reason that some orthologous genes cannot be found are mainly the two, short BAC sequences and more repeat appearing in the BACs especially in the BACs created by tetraploid.
The exon number per gene on average in each MOC1 homologous BAC is similarity with each other. High gene density is discovered in AA genome type, but one high and one low are found in tetraploid genomes except CCDD genome.
One whole cds sequences of new gene generated by de novo have been detected here. by sequence alignment, we find a short conserved DNA sequence comparison within far relative species GG, FF and EE, but the conserved sequence become longer than before gradually within more closely relative species EE and BB and the new gene which has full length cDNA support (AK062635) by 100 percent is originated eventually in AA and BB genomes.
The molecular evidence for nonfunctionalization of duplicated gene originated from whole genome duplication and/or gene duplication has been discovered from several species of Oryza. There is one homologous gene of 42DP1006 in all tetraploid Oryza species except CCDD genome has no PCR products in RT-PCR experiments although several times repeated. The homologous gene of 42DP1006 in GG genome, O. granulata, has been duplicated in series and divided by retrotransposon insertion. The upriver homologous cannot be amplified in several times RT-PCR. So, nonfunctionalization of duplicated gene can be presumed.
A tetraploid, O. alta, which has an especial gene density and expression comparing with other tetraploid in Oryza genus has been found. Both the subgenome CC and DD of O. alta have high gene density and both the orthologous gene pairs of 42DP1006 can be transcribed to some extend. Further more, the expression of orthologous gene of MOC1 PAC No.6 in O. alta is normal though the third intron of this gene is inserted by about 4kb retrotransposon. The other one of the orthologous gene pairs can be transcribed normally too.
The driving force of genome expansion of Oryza genus is the amplification of transposons and retrotransposons. we find the smaller genome size of AA(350Mb~448Mb)and FF(338Mb)possess more MITE (16~21 for AA,30 for FF)and Tc1-IS630-Pogo(18 ~34 for AA,32 for FF), but not for the larger genomes. From the aspect of LTR retrotransposon number, the reverse condition appeared comparison with above, i.e. smaller LTR retrotransposons detected in AA and FF genome than other genome types in Oryza genus. From the aspect of sequence proportion by the accumulated sequence length of transposons and retrotransposons to BAC length, the larger genome size possess high proportion of retrotransposons and less high proportion of transposons. This implies the genome expansion of Oryza genus is the result of amplification of transposons and retrotransposons. and it maybe the law of genome expansion in biology.
According to the consensus MOC1 phylogenetic tree constructed by Neighbor-Joining, Maximum Parsimony, and Minimum Evolution, the most close relative genome type with AA genome that contain cultivar rice is BB and then the CC, DD, EE, respectively. The genome type of HHJJ, HHKK, FF and GG have alienated relative with AA genome.
比较基因组学方法是一个提高基因注释准确性的强有力的手段。通过RT-PCR试验及随后测序方法发现了NCBI对粳稻日本晴的一个基因注释有误,NCBI的注释多出了一段长15个核苷酸的序列。
稻属中多数直向同源基因是很保守的,且多外显子基因的外显子-内含子结构也很保守,基因种类及其排列顺序也都表现出了较高的保守性。此外,还发现了一些个别基因组特有的基因。在本研究所有的BAC中存在直向同源基因的是MOC1和探针42DP1006所来自的基因。其它的基因只是在一些BAC中有直向同源基因,而另一些BAC中则没有,这主要是由于某些基因组类型的野生稻BAC较小,序列不够长所致,同时某些MOC1同源BAC中(尤其是四倍体)有较多的重复序列导致基因密度很低,也是该同源区所共有的直向同源基因少的重要原因。
稻属中各MOC1同源区平均每个基因的外显子数目相差不大。AA组基因密度较高,四倍体基因组中(除CCDD基因组外)两个MOC1同源BAC均表现出一个基因密度较高,而另一个基因密度很低的现象。
发现了一例整个基因序列完全从头形成的新基因产生过程。通过序列比对发现,从稻属植物中亲缘关系较远的GG基因组,开始只有一段长度有限的保守的DNA序列,到CC组保守序列逐渐变长,到BB组和AA组就形成了一个新基因,即日本晴MOC1 PAC上的第13号基因及其在AA组和BB组中的直向同源基因,该基因有全长cDNA(AK062635)支持(100%)。
在多个稻属物种中找到了基因组加倍或基因加倍后复制基因去功能化的分子证据。稻属四倍体物种中除CCDD基因组的O. alta外,探针42DP1006的两个同源基因中均有一个在多次重复RT-PCR试验中均未扩增出任何产物。GG基因组的O. granulata中,该同源基因发生了串联复制,形成前后两个同源拷贝并被逆转座子插入而分开,其中上游的拷贝在多次重复RT-PCR试验中也均未扩增出任何产物。因此,推测加倍后的复制基因发生了去功能化。
发现了一个在基因密度、基因表达上比较特殊的四倍体O. alta。在本研究所涉及的MOC1同源区内,CCDD基因组O. alta中的两套遗传物质都有较高的基因密度(CC,9.8kb/基因;DD,10.1kb/基因),且探针42DP1006的直向同源基因对都保持了一定表达能力。此外,O. alta中的日本晴MOC1 PAC上第6号基因的一个同源基因虽被长约4kb的一个逆转座子插入到第3个内含子中但并没有影响该同源基因的表达,而且该四倍体的另一个同源基因在表达上也是正常的。
稻属植物基因组膨胀的主要动力是转座子和逆转座子扩增。研究发现稻属植物中基因组较小的AA组(350Mb~448Mb)和FF组(338Mb)具有较多的MITE(AA,16个~21个;FF,30个)和Tc1-IS630-Pogo(AA,18个~34个;FF,32个);而其它基因组较大(除BB组423Mb外,均在650Mb以上)的则这两种DNA型转座子较少。从LTR型逆转座子的数量上来看,情况正好相反,即AA组、FF组较少,而其它基因组类型则较多。从转座子和逆转座子累计长度占BAC序列长度的比重上看,也表现出了较大基因组类型中逆转座子所占比重较大,且转座子所占比重也不低的趋势。这暗示,稻属植物膨胀主要是由于转座子和逆转座子扩增造成的,而且有研究表明这可能是生物界基因组膨胀的普遍规律。
用邻接法(Neighbor-Joining)、最大简约法(Maximum Parsimony)、最小进化法(Minimum Evolution)等构建的比较一致的MOC1基因进化树表明,稻属植物中与AA基因组亲缘关系较近的是BB组(包括四倍体中的BB组),其次是CC组(包括四倍体中的CC组),而后是DD组和EE组,HHJJ、HHKK、GG、FF等组与AA组间亲缘关系较远。
Tillering is the ramifying trait emerging in the period of growth of some grass species e.g. rice, wheat, et al.. Tillering that is close correlate with the creating of ideal plant shape is the main deciding factor of spike numbers and the consequent yield of rice, wheat, et al. The wild rice species distributed in the Torrid Zone and sub-Torrid Zone possess abundant genetic diversity and excellent genes that do not exist in cultivated rice varieties. So, the wild rice species become important gene pools for improving yield, grain quality, stress resistance, and other agronomic traits of cultivated rice varieties. Along with the completion of genome project of Oryza sativa L. ssp. Japonica cv. Nipponbare and Oryza sativa L. ssp. Indica cv. 93-11 and the sequencing cost dropping more and more, to do some work about comparative genomics at DNA sequence level become more and more realizable. So, in order to give some theoretical and technological support for the wild rice resources utilizing effectively, the comparative analysis among MONOCULM1 (MOC1) orthologous regions in Oryza genus has been done by employing the methods of comparative genomics at DNA sequence level and bioinformatics. The results are depicted as follows.
The comparative genomics is a strongly method to improving the veracity of gene annotation. One gene annotation error in NCBI was discovered through RT-PCR and subsequently sequencing. 15bp nucleotides in the coding sequence of this gene annotated in NCBI is excessive than the reality of this gene.
The majority of orthologous genes and the intron-exon structures of these genes in Oryza genus are much conserved and the gene contents and order is also. Some genome specific genes were found. The orthologous genes existed all over in the BACs sequenced in this research are MOC1 and the gene that probe 42DP1006 is come from on Japonica MOC1 PAC. Other genes on MOC1 PAC except the two mentioned above can be found their orthologous genes from several BACs only. The reason that some orthologous genes cannot be found are mainly the two, short BAC sequences and more repeat appearing in the BACs especially in the BACs created by tetraploid.
The exon number per gene on average in each MOC1 homologous BAC is similarity with each other. High gene density is discovered in AA genome type, but one high and one low are found in tetraploid genomes except CCDD genome.
One whole cds sequences of new gene generated by de novo have been detected here. by sequence alignment, we find a short conserved DNA sequence comparison within far relative species GG, FF and EE, but the conserved sequence become longer than before gradually within more closely relative species EE and BB and the new gene which has full length cDNA support (AK062635) by 100 percent is originated eventually in AA and BB genomes.
The molecular evidence for nonfunctionalization of duplicated gene originated from whole genome duplication and/or gene duplication has been discovered from several species of Oryza. There is one homologous gene of 42DP1006 in all tetraploid Oryza species except CCDD genome has no PCR products in RT-PCR experiments although several times repeated. The homologous gene of 42DP1006 in GG genome, O. granulata, has been duplicated in series and divided by retrotransposon insertion. The upriver homologous cannot be amplified in several times RT-PCR. So, nonfunctionalization of duplicated gene can be presumed.
A tetraploid, O. alta, which has an especial gene density and expression comparing with other tetraploid in Oryza genus has been found. Both the subgenome CC and DD of O. alta have high gene density and both the orthologous gene pairs of 42DP1006 can be transcribed to some extend. Further more, the expression of orthologous gene of MOC1 PAC No.6 in O. alta is normal though the third intron of this gene is inserted by about 4kb retrotransposon. The other one of the orthologous gene pairs can be transcribed normally too.
The driving force of genome expansion of Oryza genus is the amplification of transposons and retrotransposons. we find the smaller genome size of AA(350Mb~448Mb)and FF(338Mb)possess more MITE (16~21 for AA,30 for FF)and Tc1-IS630-Pogo(18 ~34 for AA,32 for FF), but not for the larger genomes. From the aspect of LTR retrotransposon number, the reverse condition appeared comparison with above, i.e. smaller LTR retrotransposons detected in AA and FF genome than other genome types in Oryza genus. From the aspect of sequence proportion by the accumulated sequence length of transposons and retrotransposons to BAC length, the larger genome size possess high proportion of retrotransposons and less high proportion of transposons. This implies the genome expansion of Oryza genus is the result of amplification of transposons and retrotransposons. and it maybe the law of genome expansion in biology.
According to the consensus MOC1 phylogenetic tree constructed by Neighbor-Joining, Maximum Parsimony, and Minimum Evolution, the most close relative genome type with AA genome that contain cultivar rice is BB and then the CC, DD, EE, respectively. The genome type of HHJJ, HHKK, FF and GG have alienated relative with AA genome.
引文
[1] Morishima H. Species relationships and the search for ancestors[J]. Biology of Rice[A]. Am sterdam: Tokyo/Elsevier, Tsunoda S, Takahashi Neds, 1984. 3～30.
[2] Second G. Origin of the genic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci[J]. Jpn. J. Genet., 1982, 57(6): 25～75.
[3] Dally A M, Second G. Chloroplast DNA diversity in wild and cultivated spe cies of rice (Genus Oryza, Section Oryza) cladistic mutation and genetic distance analysis[J]. Theor. Appl. Genet., 1990, 80(2): 209～222.
[4] Sarkar R, Raina S N. Assessment of genome relationships in the genus Oryza L. based on seed-protein profile analysis[J]. Theor. Appl. Genet., 1992, 85(8): 127～132.
[5] Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs[J]. Theor. Appl. Genet., 1992, 83(8): 565～581.
[6] Aggarwal R K, Brar D S, Khush G S. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization[J]. Mol. Gen. Genet., 1997, 254(1): 1～12.
[7] Prodoehl A. Oryzeae monographice describuntur[J]. BotArch, 1922, 1(2): 211～224.
[8] Roschevicz R J. A contribution to the knowledge of rice[J]. Bull. Appl. Bot. Genet. Plant Breed, 1931, 27(4): 31～33.
[9] Chatteree D. A modified key and enumeration of the species of Oryza L.[J]. Indian J. Agre. Sci., 1948, 4(13): 185～192.
[10] Sampath S. The genus Oryza: its taxonomy and species inter relationships[J]. Oryza, 1962, 1(3): 1～29.
[11] Sharma S D, Shastry S V S. Taxonomy of the genus Oryza Ⅵ. A modified classification of genus[J]. Indian J. Genet., 1965, 25(8): 173～178.
[12] Sharma S D, Shastry S V S. Evolution in genus Oryza Advancing Frontiers in Cytogenetics[J]. Proc. National Seminar[A], New Delhi: Hindustan Pub. Corp. 1972, 5～20.
[13] Shastry S V S, Sharma S D, Rao D R R. Taxonomic studies in genus Oryza[J]. Nucleus, 1961, 4(7): 67～80.
[14] Vaughan D A. The genus Oryza L.: current status of taxonomy[J]. IRPS, 1989, 138(5): 2～21.
[15] Vaughan D A. The wild Relatives of Rice: A Genetic Resources Handbook[M]. Philippines: Los Banos, IRRI, 1994, 3～8.
[16] Lu B R. Taxonomy of the genus Oryza (Poaceae): Historical perspective and current status[J]. International Rice Research Notes, 1999, 24(7): 4～8.
[17] 范树国, 张再君. 稻属植物分类研究的历史与现状[J]. 武汉植物学研究, 2000, 18(4): 329～337.
[18] 卢宝荣, 葛颂, 桑涛, 等. 稻属分类的现状及存在的问题[J]. 植物分类学报, 2001, 39(4): 373～388.
[19] 吴万春. 稻属植物分类研究的进展[J]. 华南农业大学学报, 1995, 16(4): 115～122.
[20] Chang T T. Crop history and genetic conservation: rice—a case study[J]. Iowa State J. Res., 1985, 59(6): 425～455.
[21] 张乃群. 稻属种间关系研究综论[J]. 南阳师范学院学报(自然科学版), 2002, 1(6): 61～66.
[22] 钟代彬, 罗利军. 野生稻在栽培稻育种中的应用[J]. 种子, 1995, 75(1): 25～29.
[23] Zhang Z Y, wen J, Lu B R. Diversity of leaf epidermal structures used in biosystematics of rice species[J]. International Rice Research Notes. 1997, 22(3): 4～5.
[24] 祁仲夏, 宋文芹, 金刚, 等. 稻属基因组间相关性的 AFLP 分析[J]. 南开大学学报(自然科学版), 2001, 34(3): 74～801.
[25] Nayar N M. Origin and cytogenetics of rice[J]. Adv. Genet., 1973, 17(8): 153～299.
[26] Morishima H. Species relationships and the search for ancestors[J]. Biology of Rice[A]. Am sterdam: Tokyo/Elsevier, Tsunoda S, Takahashi Neds, 1984. 3～30.
[27] Ge S, Sang T, Lu B R, et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(7): 14400～14405.
[28] Ge S, Li A, Lu B R, et al. A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data[J]. American Journal of Botany, 2002, 89(3): 1967～1972.
[29] Kurata N, Omura T. Karyotype analysis in rice 1. A new method for identifying all chromosomes pairs[J]. Japan J. Genet., 1978, 53(4): 251～255.
[30] Khush G S. Origin, dispersal, cultivation and variation of rice[J]. Plant Mol. Biol., 1997, 35(1): 25～34.
[31] Katayama T. Cytogenetical studies on the genus Oryza. I. Chromosome pairing of interspecific hybrid O.sative × O.officinalis under different temperature conditions[J]. Nippon Idengaku Zasshi, 1965, 40(6): 307～313.
[32] Katayama T, Onizuka W. Shin Y B. Intersectional F1 hybrids obtained from the crosses, Oryza minuta Presl. × O.ridleyi Hook, and O.officinalis wall. × O.ridleyi Hook[J]. Japan J. Genetics, 1981, 56(6): 67～71.
[33] 吴先军. 水稻染色体研究述评[J]. 西南农业学报, 2000, 13(2): 115～120.
[34] 谭光轩, 王红星. 野生稻亲缘关系研究进展[J]. 大自然探索, 1999, 18(1): 75～80.
[35] Hu C H. Cytogenetics studies of Oryza officinalis complex Ⅳ.F1 hybrids of O.minuta and O.grandiglumis with 4X O.officinalis[J]. Indian J. Genet. Plant Breed, 1970, 30(9): 410～417.
[36] Chevalier A. Nouvelle contribution a etude system atique des Oryza[J]. Rev. Bot. Appl. Agric. Trop, 1932, 2(7): 1014～1032.
[37] Nakano M, Yoshimura A, Iwata N. Phylogenetic study of cultivated rice and its wild relative by RFLP[J]. Rice Genetics Newsletter, 1992, 9(7): 132～134.
[38] Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs[J]. Theor. Appl. Genet., 1992, 83(8): 565～581.
[39] 周毅, 邹喻苹, 洪德元, 等. 中国野生稻及栽培稻核糖体 DNA 第一转录间隔区序列分析及其系统学意义[J]. 植物学报, 1996, 38(10): 785～791.
[40] Jena K K, Khush G S, Kochert G. Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O.sativa[J]. Genome, 1994, 37(3): 382～389.
[41] Ichikawa H, Hirai A, Katayama T. Genetic analysis of Oryza species by molecular markers for chloroplast genomes[J]. Theor. Appl. Genet., 1986, 72(9): 353～358.
[42] Oka H L, Chang W T. Rice varieties intermediate between wild cultivated rice foems the origin of the japonica type[J]. Bot. Bull. Acad. sinic., 1962, 3(5): 109～131.
[43] 丁颖. 中国栽培稻种的起源及其演变[A]. 丁颖稻作论文选集[C]. 北京: 农业出版社, 1957. 25～30.
[44] Wang X K, Sun C Q, Chai H W, et a l. The origin and evolution of rice in China[J]. Chinese Science Bulletin, 1998, 43(22): 2354～2363.
[45] Chang T T. The origin, evolution, cultivation, dissemination and diversification of Asian and African rice[J]. Ephytica, 1976, 25(8): 435～444.
[46] 丁颍. 中国栽培稻的起源和进化[J]. 农业学报, 1957, 8(3): 243～260.
[47] 周拾禄. 稻作科学技术[M]. 北京: 农业出版社出版, 1981.
[48] 程侃声, 王象坤. Ⅶ: 关于西南稻种类型的讨论[J]. 北京农业大学学报, 1985, 11(4): 239～248.
[49] 孙传清. 毛龙, 王振山, 等. 栽培稻和普通野生稻基因组的随机扩增多态性 DNA(RFLP)初步分析[J]. 中国水稻科学, 1995, 9(1): 1～6.
[50] 肖晗, 应存山, 黄大年. 中国栽培稻及其近缘野生种 cpDNA 的 RFLP 分析[J]. 中国水稻科学, 1996, 10(1): 121～124.
[51] 王振山, 陈洪, 朱立煌, 等. 中国普通野生稻遗传分化的 RAPD 研究[J]. 植物学报, 1996, 38(9): 749～752.
[52] 张祥喜, 罗林广. 野生稻优异基因分子标记定位与利用研究进展[J]. 生物技术通报, 2002, 6(8): 1～4.
[53] 杨庆文, 陈大洲. 中国野生稻研究与利用[A]. 第一届全国野生稻大会论文集[C]. 北京: 气象出版社, 2004. 26～28.
[54] 姜文正, 涂英文, 丁忠华, 等. 东乡野生稻研究[J]. 作物品种资源, 1988, 3(1): 1～4.
[55] 范树国, 张再君. 中国野生稻遗传资源的保护及其在育种中的利用[J]. 生物多样性, 2000, 8(2): 198～204.
[56] Swing J M. Reclassification of the causal agents of bacterial blight (Xoo) and bacterial leaf streak of rice[J]. Nom. Rev. J. Bacterial, 1990, 40(10): 309～311.
[57] Mew T W. Current status and future prospects of research on bacterial blight of rice[J]. Ann. Rev. Phytopatho., 1987, 125(3): 539～582.
[58] Amante Bordeos A, Sitch L A, Nelson R, et al. Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice, Oryza sativa[J]. Theor. Appl. Genet., 1992, 84(34): 345～354.
[59] 颜辉煌, 胡慧英, 傅强, 等. 栽培稻与药用野生稻杂种后代的形态学和细胞遗传学研究[J]. 中国水稻科学, 1996, 10(3): 138～142.
[60] 钟代彬, 罗利军, 郭龙彪, 等. 栽野杂交转移药用野生稻抗褐飞虱基因[J]. 西南农业学报, 1997, 10(2): 5～9.
[61] 秦学毅, 韦素美. 普通野生稻抗褐稻虱基因导入栽培稻研究[J]. 广西农业科学, 2002, 12(2): 57～59.
[62] 覃瑞, 魏文辉, 宁顺斌, 等. 利用水稻BAC克隆对Gm-2和Gm-6在药用野生稻中的FISH定位[J]. 中国农业科学, 2001, 34 (1): 1～4.
[63] 陈大洲, 邓仁根, 肖叶青, 等. 东乡野生稻抗寒基因的利用与发展前景[J]. 江西农业学报, 1998, 10(1): 65～68.
[64] Bay D Nguyen, Darshan S Brar, Buu C Bui, et al. Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff, into indica rice (oryza sativa L.)[J]. Theor. Appl. Genet., 2003, 106(6): 583～593.
[65] 庞汉华. 栽培稻与野生稻杂交花培创新种质的研究[J]. 作物品种资源, 1999, (2): 10～12.
[66] 李德军, 孙传清, 付永彩, 等. 利用 AB-QTL 法定位江西东乡野生稻中的高产基因[J]. 科学通报, 2002, 47(11): 854～858.
[67] Xiao J, Grandillo S, Ahn S N, et al. Gene from wild rice improve yield[J]. Nature, 1996, 384(10): 223～224.
[68] 秦前锦, 李桂菊. 野生稻资源的特异性状与超高产育种[J]. 湖北农业科学, 2000, (6): 16～18.
[69] Sitch L A, Dalmacio R, Brar B S, et al. Identification and transfer of a new cytoplasmic male sterility source form Oryza perennis into indica rice(O.sativa)[J]. Rice Genetics Newsletter, 1991, 8(10): 93～94.
[70] 刘雪贞, 潘大建, 吴惟瑞, 等. 广东普通野生稻雄性不育性的利用研究[J]. 广东农业科学, 2001, 4(3): 7～9.
[71] 钟代彬,罗利军, 应存山, 等. 野生稻有利基因转移研究进展[J]. 中国水稻科学, 2000, 14(2): 103～106.
[72] Dally A M, Second G. Chloroplast DNA diversity in wild and cultivated spe cies of rice (Genus Oryza, Section Oryza) cladistic mutation and genetic distance analysis[J]. Theor. Appl. Genet., 1990, 80(2): 209～222.
[73] 张尚宏. 五种野生稻叶绿体 DNA 多态性研究[J]. 遗传, 1996, 18(I): 15～18.
[74] 角田重三郎, 高桥成人. 水稻生物学(武汉大学生物系遗传研究室译) [M]. 武汉: 武汉大学出版社, 1988. 1～37.
[75] Bonierbale M W, Plaisted R L, Tanksley S D. RFLP maps based on a common set of clones reveal modes of chromosomes evolution in potato and tomato[J]. Genetics, 1988, 120(4): 1095～1103.
[76] Chao S, Sharp P J, Gale M D. A linkage map of wheat homoeologous group 7 chromosomes using RFLP markers[J]. In Proc. 7th Int. Wheat Genet. Symp.[C], eds. Miller T E, Koebner R M D. (IPSR, Cambridge Laboratory, Cambridge), 1988(4). 493～498.
[77] Ahn S N, Tanksley S D. Comparative linkage maps of the rice and maize genomes[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(17): 7980～7984.
[78] Kurata N, Moore G, Nagamura Y, et al. Conservation of genome structure between rice and wheat[J]. BioTechnology, 1994, 12(13): 276～278.
[79] Devos K M, Chao S, Li Q Y, et al. Relationship between chromosome 9 of maize and wheat homeologous group 7 chromosomes[J]. Genetics, 1994, 138(4): 1287～1292.
[80] Grivet L D, Hont A, Dufour P, et al. Comparative genome mapping of sugarcane with other species within the Andropogoneae tribe[J]. Heredity, 1994, 73(12): 500～508.
[81] Van Deynze A E, Nelson J C, O’Donoughue L S, et al. Comparative mapping in grasses Oat relationships[J]. Mol. Gen. Genet. 1995, 249(3): 349～356.
[82] Devos K M, Wang Z M, Beales J, et al. Comparative genetic maps of foxtail millet (Setaia italica) and (Oryza sativa)[J]. Theor. Appl. Genet., 1998, 96(8): 63～68
[83] Moore G, Devos K M, Wang Z, et al. Cereal Genome Evolution: Grasses, line up and form a circle[J]. Curr. Biol., 1995, 5(7): 737～739.
[84] Gale M D, Devos K M. Plant comparative genetics after 10 years[J]. Science, 1998, 282(5389): 656～659.
[85] Chen M, SanMiguel P, De Oliveira A C, etal. Microcolinearity in sh2-homologous regions of maize, rice, and sorghum genomes[J]. Proc. Natl. Acad. Sci. USA, 1997, 94(7): 3431～3435.
[86] Renato T, Phyllis B, Robin W, et al. The Complete Sequence of 340 kb of DNA around the Rice Adh1/Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4[J]. The Plant Cell, 2000, 12(3): 381～391.
[87] Brunner S, Keller B, Feuillet C. A large rearrangement involving genes and low copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus[J]. Genetics, 2003, 164(2): 673～683.
[88] Olson M, Hood L, Cantor C, et al. A Common Language for physical mapping of the human genome[J]. Science Washington D C, 1989, 254(6): 1434～1435.
[89] Feuillet C, Keller B. High gene density is conserved at syntenic loci of small and large grass genomes[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(26): 8265～8270.
[90] Ramakrishna W J, Dubcovsky Y J, Park C, et al. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes[J]. Genetics, 2002, 162(3): 1389～1400.
[91] Song R, Messing J. Contiguous genomic DNA sequence comprising the 19kD zein gene family from maize[J]. Plant Physiol., 2002, 130(4): 1626～1635.
[92] Ramakrishna W, Emberton J, SanMiguel P, et al. Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex[J]. Plant Physiol., 2002, 130(4): 1728～1738.
[93] Langham R J, Walsh J, Dunn M, et al. Genomic duplication, fractionation and the origin of regulatory novelty[J]. Genetics, 2004, 166(2): 935～945.
[94] Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements[J]. Genetics, 1998, 150(7): 1217～1228.
[95] Koch M, Bishop J, MitchellOlds T. Molecular systematics and evolution Arabidopsis and Arabis[J]. Plant Biol., 1999, 1(4): 529～537.
[96] Boivin K, Acarkan A, Mbulu R S, et al. The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes[J]. Plant Physiol., 2004, 135(8): 735～744.
[97] Kuittinen H, Haan D, Vogl A A, et al. Comparing the linkage maps of the close relatives Arabidopsis lyrata and Arabidopsis thaliana[J]. Genetics, 2004, 168(3): 1575～1584.
[98] Marcus A K, Markus K. genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species capsella rubella, Arabidopsis lyrata subsp. petraea, and a. thaliana[J]. American Journal of Botany, 2005, 92(4): 761～767.
[99] Warwick S I, Black L D. Molecular phylogenies from theory to application in Brassica and allies (tribe Brassiceae, Brassicaceae)[J]. Opera Bot., 1997, 132(5): 159～168.
[100] Lysak M A, Koch M A, Pecinka A, et al. Chromosome triplication found across the tribe Brassiceae[J]. Genome Res., 2005, 15(9): 516～525.
[101] Christopher D T, Cheung F, Maiti R, et al. Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy[J]. The PlantCell, 2006, 18(6): 1348～1359.
[102] Yang T J, Kim J S, Kwon S J, et al. Sequence Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa[J]. The Plant Cell, 2006, 18(6): 1339～1347.
[103] Yang Y W, Lai K N, Tai P Y, et al. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages[J]. J. Mol. Evol., 1999, 48(5): 597～604.
[104] Zhang M Q. Computational prediction of eukaryotic protein coding genes[J]. Nature, 2002, 3(9): 698～709.
[105] Salamov A, Solovyev V. An initio gene finding in Drosophila genomic DNA[J]. Genome Res., 2000, 10(4): 516～522.
[106] Burge C, Karlin S. Prediction of complete gene structure in human genomic DNA[J]. Journal of Molecular Biology, 1997, 268(12): 78～94.
[107] Lomsadze A, Terhovhannisyan V, Chernoff Y, et al. Gene identification in novel eukaryotic genomes by self-training algorithm[J]. Nucl. Acid. Res., 2005, 33(20): 6494～6506.
[108] Kulp D, Haussler D, Reese M G, et al. A generalized hidden Markov model for the recognition of human genes in DNA[J]. Intell. Syst. Mol. Biol., 1996, 4: 134～142.
[109] Solovyev V, Salamov V A A, Lawrence C B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames[J]. Nucl. Acid. Res., 1994, 22(24): 5156～5163.
[110] Borodovsky M, McIninch J. GENMARK: parallel gene recognition for both DNA strands[J]. Comp. Chem., 1993, 17(7): 123～133.
[111] Parsons J D. Miropeats: graphical DNA sequence comparisons[J]. Comput. Appl. Biosci., 1995, 11(6): 615～619.
[112] Kurtz S, Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes[J]. Bioinformatics, 1999, 15(5): 426～427. Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high density picolitre reactors[J]. Nature, 2005, 437(7057): 376～380.
[113] Lander E S, Linton L M, Birren B, et al. Initial sequencing and analysis of the human genome[J]. Nature, 2001, 409(6822): 860～921.
[114] Gaut B S, Doebley J F. DNA sequence evidence for the segmental allopolyploid origin of maize[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(5): 6808～6814.
[115] Shoemaker R C, Polzin K, Labate J, et al. Gemome duplication in soybean(Glycine subgenus soja)[J]. Genetics, 1996, 144(13): 329～338.
[116] Lagercrantz U, Lydiate D. Comparative genome mapping in Brassica[J]. Genetics, 1996, 144(4): 1903～l9l0.
[117] Tian C G, Xiong Y Q, Liu T Y, et al. Evidence for an ancient whole genome duplication event in rice and other cereals[J]. Chin. J. Genet., 2005, 32(5): 519～527.
[118] Kellogg E A. Relationships of cereal crops and other grasses[J]. Proc. Nati. Acad. Sci. USA, 1998, 95(5): 2005～2010.
[119] Kellogg E A. The grasses: a case study in macroevolution[J]. Annu. Rev. Ecol. Syst., 2000, 31(9):217～238.
[120] Gilbert W. Why genes in pieces[J]. Nature, 1978, 271(5645): 501.
[121] Patthy L. Exon shuffling and other ways of module exchange[J]. Matrix Biol., 1996, 15(5): 301～312.
[122] Rijk V A, Bloemendal H. Molecular mechanisms of exon shuffling: illegitimate recombination[J]. Genetica, 2003, 118(2-3): 245～249.
[123] Rijk V A, Jong W, Bloemendal H. Exon shuffling mimicked in cell culture[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(14): 8074～8079.
[124] Moran J, DeBerardinis V, Kazazian R J, et al. Exon shuffling by L1 retrotransposition[J]. Science, 1999, 283(5407): 1530～1534.
[125] Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes[J]. Nature Genet., 2000, 24(4): 363～367.
[126] Kaessmann H, Zollner S, Nekrutenko A, et al. Signatures of domain shuffling in the human genome[J]. Genome Res., 2002, 12(11): 1642～1650.
[127] Souza S J, Long M, Schoenbach L, et al. Intron positions correlate with module boundaries in ancient proteins[J]. Proc. Nati. Acad. Sci. USA, 1996, 93(25): 14632～14636.
[128] Ohno S. Evolution by Gene Duplication[M]. Berlin: Springer, 1970.
[129] Kimura M. The Neutral Theory of Molecular Evolution[M]. Cambridge: Cambridge Univ. Press, 1983.
[130] Prince V E, Pickett F B. Splitting pairs: the diverging fates of duplicated genes[J]. Nature Rev. Genet., 2002, 3(11): 827～837.
[131] Bailey J A, Gu Z, Clark R A, et al. Recent segmental duplications in the human genome[J]. Science, 2002, 297(5583): 1003～1007.
[132] Samonte R V, Eichler E E. Segmental duplications and the evolution of the primate genome[J]. Nature Rev. Genet., 2002, 3(1): 65～72.
[133] Wang W, Brunet F G, Nevo E, et al. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster[J]. Proc. Nati. Acad. Sci. USA, 2002, 99(7): 4448～4453.
[134] Betrán E, Wang W, Jin L, et al. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene[J]. Mol. Biol. Evol. ,2002, 19(5): 654～663.
[135] Betrán E, Long M. Expansion of genome coding regions by acquisition of new genes[J]. Genetica , 2002, 115(1): 65～80.
[136] Pickeral O K, Makalowski W, Boguski M S, et al. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition[J]. Genome Res., 2000, 10(4): 411～415.
[137] Makalowski W, Mitchell G A, Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability[J]. Trends Genet, 1994, 10(6): 188～193.
[138] Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein coding genes[J]. Trends Genet., 2001, 17(6): 619～621.
[139] Sorek R, Ast G, Graur D. Alu containing exons are alternatively spliced[J]. Genome Res., 2002, 12(7): 1060～1067.
[140] Makalowski W. Genomic scrap yard: how genomes utilize all that junk[J]. Gene, 2000, 259(15):61～67.
[141] Lorenc A, Makalowski W. Transposable elements and vertebrate protein diversity[J]. Genetica, 2003, 118(2-3): 183～191.
[142] Ochman H. Lateral and oblique gene transfer[J]. Curr. Opin. Genet. Dev., 2001, 11(6): 616～619.
[143] De Koning A P, Brinkman F S, Jones S J, et al. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis[J]. Mol. Biol. Evol., 2000, 17(11): 1769～1773.
[144] Bergthorsson U, Adams K L, Thomason B, et al. Widespread horizontal transfer of mitochondrial genes in flowering plants[J]. Nature, 2003, 424(6945): 197～201.
[145] Thomson T M, Lozano J J, Loukili N, et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene[J]. Genome Res., 2000, 10(11): 1743～1756.
[146] Ranz J M, Ponce A R, Hartl D L, et al. Origin and evolution of a new gene expressed in the Drosophila sperm axoneme[J]. Genetica, 2003, 118(2-3): 233～244.
[147] McCarthy A D, Hardie D G. Fatty acid synthase an example of protein evolution by gene fusion[J]. Trends Biochem. Sci., 1984, 4(5): 60～63.
[148] Snel B, Bork P, Huynen M. Gene fusion versus gene fission[J]. Trends Genet., 2000 16(1): 9～11.
[149] Nurminsky D I, Nurminskaya M V, De Aguiar D, et al. Selective sweep of a newly evolved sperm specific gene in Drosophila[J]. Nature, 1998, 396(6711): 572～575.
[150] Chen L, DeVries A L, Cheng C H. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(8): 3817～3822.
[151] Chen L, DeVries A L, Cheng C H. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(8): 3811～3816.
[152] Martignetti J A, Brosius J. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(6): 9698～9702.
[153] Martignetti J A, Brosius J. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(24): 11563～11567.
[154] Long M, Langley C H. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila[J]. Science, 1993, 260(5104): 91～95.
[155] Begun D J. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila[J]. Genetics, 1997, 145(2): 375～382.
[156] Malik H S, Henikoff S. Adaptive evolution of Cid, a centromere specific histone in Drosophila[J]. Genetics, 2001, 157(3): 1293～1298.
[157] Betrán E, Long M. Dntf-2r: a young Drosophila retroposed gene with specific male expression under positive Darwinian selection[J]. Genetics, 2003, 164(3): 977～988.
[158] Zhang J, Zhang Y P, Rosenberg H F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey[J]. Nat. Genet., 2002, 30(4): 411～415.
[159] Zhang J, Webb D M, Podlaha O. Accelerated protein evolution and origins of human specific features: Foxp2 as an example[J]. Genetics, 2002, 162(4): 1825～1835.
[160] Enard W, Przeworski M, Fisher S E, et al. Molecular evolution of FOXP2, a gene involved in speech and language[J]. Nature, 2002, 418(6900): 869～872.
[161] Courseaux A, Nahon J L. Birth of two chimeric genes in the Hominidae lineage[J]. Science, 2001, 291(5507): 1293～1297.
[162] Johnson M E, Viggiano L, Bailey J A, et al. Positive selection of a gene family during the emergence of humans and African apes[J]. Nature, 2001, 413(6855): 514～519.
[163] Paulding C A, Ruvolo M, Haber D A. The Tre2 (USP6) oncogene is a hominoid specific gene[J]. Proc. Nati. Acad. Sci. USA, 2003, 100(8): 2507～2511.
[164] Javaud C, Dupuy F, Maftah A, et al. The fucosyltransferase gene family: an amazing summary of the underlying mechanisms of gene evolution[J]. Genetica, 2003, 118(2-3): 157～170.
[165] Maston G A, Ruvolo M. Chorionic gonadotropin has a recent origin within primates and an evolutionary history of selection[J]. Mol. Biol. Evol., 2002, 19(9): 320～335.
[166] Brosius J. The contribution of RNAs and retroposition to evolutionary novelties[J]. Genetica, 2003, 118(2-3): 99～116.
[167] Brosius J, Gould S J. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA”[J]. Proc. Nati. Acad. Sci. USA, 1992, 89(22): 10706～10710.
[168] Gogolevskaya I K, Kramerov D A. Evolutionary history of 4.5SI RNA and indication that it is functional[J]. J. Mol. Evol., 2002, 54(3): 354～364.
[169] Long M, De Souza S J, Rosenberg C, et al. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor[J]. Proc. Nati. Acad. Sci. USA, 1996, 93(15): 7727～7731.
[170] Majoros W H, Pertea M, Antonescu C, et al. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders[J]. Nucl. Acid. Res., 2003, 31(13): 3601～3604.
[171] Leutwiler L S, Hough E B R, Meyerowitz E M. The DNA of Arabidopsis thaliana[J]. Mol. Gen. Genet., 1984, 194(6): 15～23.
[172] Flavell R. Repetitive DNA and chromosome evolution in plants[J]. Philos. Trans. R. Soc. Lond. B., 1986, 312(1154): 227～242.
[173] Takashi M, Wu J Z, Hiroyuki K, et al. The map-based sequence of the rice genome[J]. Nature, 2005, 436(7052): 793～800.
[174] Yu J, Hu S N, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica)[J]. Science, 2002, 296(5565): 79～92.
[175] Goff S A, Ricke D, Lan T H, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)[J]. Science, 2002, 296(5565): 92～100.
[176] Sasaki T, Matsumoto T, Yamamoto K, et al. The genome sequence and structure of rice chromosome 1[J]. Nature, 2002, 420(6913): 312～316.
[177] Pertea M, Salzberg S L. Computational gene finding in plants[J]. Plant Mo1. Bio1., 2002, 48(1-2): 39～48.
[178] Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4[J]. Nature, 2002, 420(6913): 316～320.
[179] SanMiguel P J, Ramakrishna W, Bennetzen J L, et al. Transposable elements, genes and recombination in a 215kb contig from wheat chromosome 5A(m)[J]. Funct. Integr. Genomics, 2002, 2(1-2): 70～80.
[180] Nathalie P, Stephane R, Patrice D, et al. Evaluation of gene prediction software using a genomicdata set: application to Arabidopsis thaliana sequences[J]. Bioinformatics, 1999, 15(7): 887～899.
[181] Burset M, Guigo R. Evaluation of Gene Structure Prediction Programs[J]. Genomics, 1996, 34(3): 353～367.
[182] Salzberg S L, Delcher A L, Kasif S, et al. Microbial gene identification using interpolated Markov models[J]. Nucl. Acid. Res., 1998, 26(5): 544～548.
[183] Werner T. Models for prediction and recognition of eukaryotic promoters[J]. Mamm. Genome, 1999, 10(2): 168～175.
[184] Masterson J. Stomatal size in fossil plants: Evidence for polyploid in majority of angiosperms[J]. Science, 1994, 264(5146): 421～424.
[185] Lee H S, Chen Z J. Protein coding genes are epigenetically regulated in Arabidopsis polyploids[J]. Proc. Nati. Acad. Sci. USA, 2001, 98(12): 6753～6758.
[186] Kashkush K, Feldman M, Levy A A. Gene loss, silencing and activation in newly synthesized wheat allopolyploid[J]. Genetics, 2002, 160(4): 1651～1659.
[187] Adams K L, Percifield R, Wendek J F. Organ specific silencing of duplicated genes in a newly synthesized cotton allotetraploid[J]. Genetics, 2004, 168(4): 2217～2226.
[188] Comai L, Tyagi A P, Winter K, et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids[J]. Plant Cell, 2000, 12(9): 1551～1568.
[189] Kashkush K, Feldman M, Levy A A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat[J]. Nat. Genet., 2003, 33(1): 102～106.
[190] He P, Friebe B R, Gill B S, et al. Allopolyploidy alters gene expression in the highly stable hexaploid wheat[J]. Plant Mo1. Bio1., 2003, 52(2): 401～4l4.
[2] Second G. Origin of the genic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci[J]. Jpn. J. Genet., 1982, 57(6): 25～75.
[3] Dally A M, Second G. Chloroplast DNA diversity in wild and cultivated spe cies of rice (Genus Oryza, Section Oryza) cladistic mutation and genetic distance analysis[J]. Theor. Appl. Genet., 1990, 80(2): 209～222.
[4] Sarkar R, Raina S N. Assessment of genome relationships in the genus Oryza L. based on seed-protein profile analysis[J]. Theor. Appl. Genet., 1992, 85(8): 127～132.
[5] Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs[J]. Theor. Appl. Genet., 1992, 83(8): 565～581.
[6] Aggarwal R K, Brar D S, Khush G S. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization[J]. Mol. Gen. Genet., 1997, 254(1): 1～12.
[7] Prodoehl A. Oryzeae monographice describuntur[J]. BotArch, 1922, 1(2): 211～224.
[8] Roschevicz R J. A contribution to the knowledge of rice[J]. Bull. Appl. Bot. Genet. Plant Breed, 1931, 27(4): 31～33.
[9] Chatteree D. A modified key and enumeration of the species of Oryza L.[J]. Indian J. Agre. Sci., 1948, 4(13): 185～192.
[10] Sampath S. The genus Oryza: its taxonomy and species inter relationships[J]. Oryza, 1962, 1(3): 1～29.
[11] Sharma S D, Shastry S V S. Taxonomy of the genus Oryza Ⅵ. A modified classification of genus[J]. Indian J. Genet., 1965, 25(8): 173～178.
[12] Sharma S D, Shastry S V S. Evolution in genus Oryza Advancing Frontiers in Cytogenetics[J]. Proc. National Seminar[A], New Delhi: Hindustan Pub. Corp. 1972, 5～20.
[13] Shastry S V S, Sharma S D, Rao D R R. Taxonomic studies in genus Oryza[J]. Nucleus, 1961, 4(7): 67～80.
[14] Vaughan D A. The genus Oryza L.: current status of taxonomy[J]. IRPS, 1989, 138(5): 2～21.
[15] Vaughan D A. The wild Relatives of Rice: A Genetic Resources Handbook[M]. Philippines: Los Banos, IRRI, 1994, 3～8.
[16] Lu B R. Taxonomy of the genus Oryza (Poaceae): Historical perspective and current status[J]. International Rice Research Notes, 1999, 24(7): 4～8.
[17] 范树国, 张再君. 稻属植物分类研究的历史与现状[J]. 武汉植物学研究, 2000, 18(4): 329～337.
[18] 卢宝荣, 葛颂, 桑涛, 等. 稻属分类的现状及存在的问题[J]. 植物分类学报, 2001, 39(4): 373～388.
[19] 吴万春. 稻属植物分类研究的进展[J]. 华南农业大学学报, 1995, 16(4): 115～122.
[20] Chang T T. Crop history and genetic conservation: rice—a case study[J]. Iowa State J. Res., 1985, 59(6): 425～455.
[21] 张乃群. 稻属种间关系研究综论[J]. 南阳师范学院学报(自然科学版), 2002, 1(6): 61～66.
[22] 钟代彬, 罗利军. 野生稻在栽培稻育种中的应用[J]. 种子, 1995, 75(1): 25～29.
[23] Zhang Z Y, wen J, Lu B R. Diversity of leaf epidermal structures used in biosystematics of rice species[J]. International Rice Research Notes. 1997, 22(3): 4～5.
[24] 祁仲夏, 宋文芹, 金刚, 等. 稻属基因组间相关性的 AFLP 分析[J]. 南开大学学报(自然科学版), 2001, 34(3): 74～801.
[25] Nayar N M. Origin and cytogenetics of rice[J]. Adv. Genet., 1973, 17(8): 153～299.
[26] Morishima H. Species relationships and the search for ancestors[J]. Biology of Rice[A]. Am sterdam: Tokyo/Elsevier, Tsunoda S, Takahashi Neds, 1984. 3～30.
[27] Ge S, Sang T, Lu B R, et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(7): 14400～14405.
[28] Ge S, Li A, Lu B R, et al. A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data[J]. American Journal of Botany, 2002, 89(3): 1967～1972.
[29] Kurata N, Omura T. Karyotype analysis in rice 1. A new method for identifying all chromosomes pairs[J]. Japan J. Genet., 1978, 53(4): 251～255.
[30] Khush G S. Origin, dispersal, cultivation and variation of rice[J]. Plant Mol. Biol., 1997, 35(1): 25～34.
[31] Katayama T. Cytogenetical studies on the genus Oryza. I. Chromosome pairing of interspecific hybrid O.sative × O.officinalis under different temperature conditions[J]. Nippon Idengaku Zasshi, 1965, 40(6): 307～313.
[32] Katayama T, Onizuka W. Shin Y B. Intersectional F1 hybrids obtained from the crosses, Oryza minuta Presl. × O.ridleyi Hook, and O.officinalis wall. × O.ridleyi Hook[J]. Japan J. Genetics, 1981, 56(6): 67～71.
[33] 吴先军. 水稻染色体研究述评[J]. 西南农业学报, 2000, 13(2): 115～120.
[34] 谭光轩, 王红星. 野生稻亲缘关系研究进展[J]. 大自然探索, 1999, 18(1): 75～80.
[35] Hu C H. Cytogenetics studies of Oryza officinalis complex Ⅳ.F1 hybrids of O.minuta and O.grandiglumis with 4X O.officinalis[J]. Indian J. Genet. Plant Breed, 1970, 30(9): 410～417.
[36] Chevalier A. Nouvelle contribution a etude system atique des Oryza[J]. Rev. Bot. Appl. Agric. Trop, 1932, 2(7): 1014～1032.
[37] Nakano M, Yoshimura A, Iwata N. Phylogenetic study of cultivated rice and its wild relative by RFLP[J]. Rice Genetics Newsletter, 1992, 9(7): 132～134.
[38] Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs[J]. Theor. Appl. Genet., 1992, 83(8): 565～581.
[39] 周毅, 邹喻苹, 洪德元, 等. 中国野生稻及栽培稻核糖体 DNA 第一转录间隔区序列分析及其系统学意义[J]. 植物学报, 1996, 38(10): 785～791.
[40] Jena K K, Khush G S, Kochert G. Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O.sativa[J]. Genome, 1994, 37(3): 382～389.
[41] Ichikawa H, Hirai A, Katayama T. Genetic analysis of Oryza species by molecular markers for chloroplast genomes[J]. Theor. Appl. Genet., 1986, 72(9): 353～358.
[42] Oka H L, Chang W T. Rice varieties intermediate between wild cultivated rice foems the origin of the japonica type[J]. Bot. Bull. Acad. sinic., 1962, 3(5): 109～131.
[43] 丁颖. 中国栽培稻种的起源及其演变[A]. 丁颖稻作论文选集[C]. 北京: 农业出版社, 1957. 25～30.
[44] Wang X K, Sun C Q, Chai H W, et a l. The origin and evolution of rice in China[J]. Chinese Science Bulletin, 1998, 43(22): 2354～2363.
[45] Chang T T. The origin, evolution, cultivation, dissemination and diversification of Asian and African rice[J]. Ephytica, 1976, 25(8): 435～444.
[46] 丁颍. 中国栽培稻的起源和进化[J]. 农业学报, 1957, 8(3): 243～260.
[47] 周拾禄. 稻作科学技术[M]. 北京: 农业出版社出版, 1981.
[48] 程侃声, 王象坤. Ⅶ: 关于西南稻种类型的讨论[J]. 北京农业大学学报, 1985, 11(4): 239～248.
[49] 孙传清. 毛龙, 王振山, 等. 栽培稻和普通野生稻基因组的随机扩增多态性 DNA(RFLP)初步分析[J]. 中国水稻科学, 1995, 9(1): 1～6.
[50] 肖晗, 应存山, 黄大年. 中国栽培稻及其近缘野生种 cpDNA 的 RFLP 分析[J]. 中国水稻科学, 1996, 10(1): 121～124.
[51] 王振山, 陈洪, 朱立煌, 等. 中国普通野生稻遗传分化的 RAPD 研究[J]. 植物学报, 1996, 38(9): 749～752.
[52] 张祥喜, 罗林广. 野生稻优异基因分子标记定位与利用研究进展[J]. 生物技术通报, 2002, 6(8): 1～4.
[53] 杨庆文, 陈大洲. 中国野生稻研究与利用[A]. 第一届全国野生稻大会论文集[C]. 北京: 气象出版社, 2004. 26～28.
[54] 姜文正, 涂英文, 丁忠华, 等. 东乡野生稻研究[J]. 作物品种资源, 1988, 3(1): 1～4.
[55] 范树国, 张再君. 中国野生稻遗传资源的保护及其在育种中的利用[J]. 生物多样性, 2000, 8(2): 198～204.
[56] Swing J M. Reclassification of the causal agents of bacterial blight (Xoo) and bacterial leaf streak of rice[J]. Nom. Rev. J. Bacterial, 1990, 40(10): 309～311.
[57] Mew T W. Current status and future prospects of research on bacterial blight of rice[J]. Ann. Rev. Phytopatho., 1987, 125(3): 539～582.
[58] Amante Bordeos A, Sitch L A, Nelson R, et al. Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice, Oryza sativa[J]. Theor. Appl. Genet., 1992, 84(34): 345～354.
[59] 颜辉煌, 胡慧英, 傅强, 等. 栽培稻与药用野生稻杂种后代的形态学和细胞遗传学研究[J]. 中国水稻科学, 1996, 10(3): 138～142.
[60] 钟代彬, 罗利军, 郭龙彪, 等. 栽野杂交转移药用野生稻抗褐飞虱基因[J]. 西南农业学报, 1997, 10(2): 5～9.
[61] 秦学毅, 韦素美. 普通野生稻抗褐稻虱基因导入栽培稻研究[J]. 广西农业科学, 2002, 12(2): 57～59.
[62] 覃瑞, 魏文辉, 宁顺斌, 等. 利用水稻BAC克隆对Gm-2和Gm-6在药用野生稻中的FISH定位[J]. 中国农业科学, 2001, 34 (1): 1～4.
[63] 陈大洲, 邓仁根, 肖叶青, 等. 东乡野生稻抗寒基因的利用与发展前景[J]. 江西农业学报, 1998, 10(1): 65～68.
[64] Bay D Nguyen, Darshan S Brar, Buu C Bui, et al. Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff, into indica rice (oryza sativa L.)[J]. Theor. Appl. Genet., 2003, 106(6): 583～593.
[65] 庞汉华. 栽培稻与野生稻杂交花培创新种质的研究[J]. 作物品种资源, 1999, (2): 10～12.
[66] 李德军, 孙传清, 付永彩, 等. 利用 AB-QTL 法定位江西东乡野生稻中的高产基因[J]. 科学通报, 2002, 47(11): 854～858.
[67] Xiao J, Grandillo S, Ahn S N, et al. Gene from wild rice improve yield[J]. Nature, 1996, 384(10): 223～224.
[68] 秦前锦, 李桂菊. 野生稻资源的特异性状与超高产育种[J]. 湖北农业科学, 2000, (6): 16～18.
[69] Sitch L A, Dalmacio R, Brar B S, et al. Identification and transfer of a new cytoplasmic male sterility source form Oryza perennis into indica rice(O.sativa)[J]. Rice Genetics Newsletter, 1991, 8(10): 93～94.
[70] 刘雪贞, 潘大建, 吴惟瑞, 等. 广东普通野生稻雄性不育性的利用研究[J]. 广东农业科学, 2001, 4(3): 7～9.
[71] 钟代彬,罗利军, 应存山, 等. 野生稻有利基因转移研究进展[J]. 中国水稻科学, 2000, 14(2): 103～106.
[72] Dally A M, Second G. Chloroplast DNA diversity in wild and cultivated spe cies of rice (Genus Oryza, Section Oryza) cladistic mutation and genetic distance analysis[J]. Theor. Appl. Genet., 1990, 80(2): 209～222.
[73] 张尚宏. 五种野生稻叶绿体 DNA 多态性研究[J]. 遗传, 1996, 18(I): 15～18.
[74] 角田重三郎, 高桥成人. 水稻生物学(武汉大学生物系遗传研究室译) [M]. 武汉: 武汉大学出版社, 1988. 1～37.
[75] Bonierbale M W, Plaisted R L, Tanksley S D. RFLP maps based on a common set of clones reveal modes of chromosomes evolution in potato and tomato[J]. Genetics, 1988, 120(4): 1095～1103.
[76] Chao S, Sharp P J, Gale M D. A linkage map of wheat homoeologous group 7 chromosomes using RFLP markers[J]. In Proc. 7th Int. Wheat Genet. Symp.[C], eds. Miller T E, Koebner R M D. (IPSR, Cambridge Laboratory, Cambridge), 1988(4). 493～498.
[77] Ahn S N, Tanksley S D. Comparative linkage maps of the rice and maize genomes[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(17): 7980～7984.
[78] Kurata N, Moore G, Nagamura Y, et al. Conservation of genome structure between rice and wheat[J]. BioTechnology, 1994, 12(13): 276～278.
[79] Devos K M, Chao S, Li Q Y, et al. Relationship between chromosome 9 of maize and wheat homeologous group 7 chromosomes[J]. Genetics, 1994, 138(4): 1287～1292.
[80] Grivet L D, Hont A, Dufour P, et al. Comparative genome mapping of sugarcane with other species within the Andropogoneae tribe[J]. Heredity, 1994, 73(12): 500～508.
[81] Van Deynze A E, Nelson J C, O’Donoughue L S, et al. Comparative mapping in grasses Oat relationships[J]. Mol. Gen. Genet. 1995, 249(3): 349～356.
[82] Devos K M, Wang Z M, Beales J, et al. Comparative genetic maps of foxtail millet (Setaia italica) and (Oryza sativa)[J]. Theor. Appl. Genet., 1998, 96(8): 63～68
[83] Moore G, Devos K M, Wang Z, et al. Cereal Genome Evolution: Grasses, line up and form a circle[J]. Curr. Biol., 1995, 5(7): 737～739.
[84] Gale M D, Devos K M. Plant comparative genetics after 10 years[J]. Science, 1998, 282(5389): 656～659.
[85] Chen M, SanMiguel P, De Oliveira A C, etal. Microcolinearity in sh2-homologous regions of maize, rice, and sorghum genomes[J]. Proc. Natl. Acad. Sci. USA, 1997, 94(7): 3431～3435.
[86] Renato T, Phyllis B, Robin W, et al. The Complete Sequence of 340 kb of DNA around the Rice Adh1/Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4[J]. The Plant Cell, 2000, 12(3): 381～391.
[87] Brunner S, Keller B, Feuillet C. A large rearrangement involving genes and low copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus[J]. Genetics, 2003, 164(2): 673～683.
[88] Olson M, Hood L, Cantor C, et al. A Common Language for physical mapping of the human genome[J]. Science Washington D C, 1989, 254(6): 1434～1435.
[89] Feuillet C, Keller B. High gene density is conserved at syntenic loci of small and large grass genomes[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(26): 8265～8270.
[90] Ramakrishna W J, Dubcovsky Y J, Park C, et al. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes[J]. Genetics, 2002, 162(3): 1389～1400.
[91] Song R, Messing J. Contiguous genomic DNA sequence comprising the 19kD zein gene family from maize[J]. Plant Physiol., 2002, 130(4): 1626～1635.
[92] Ramakrishna W, Emberton J, SanMiguel P, et al. Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex[J]. Plant Physiol., 2002, 130(4): 1728～1738.
[93] Langham R J, Walsh J, Dunn M, et al. Genomic duplication, fractionation and the origin of regulatory novelty[J]. Genetics, 2004, 166(2): 935～945.
[94] Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements[J]. Genetics, 1998, 150(7): 1217～1228.
[95] Koch M, Bishop J, MitchellOlds T. Molecular systematics and evolution Arabidopsis and Arabis[J]. Plant Biol., 1999, 1(4): 529～537.
[96] Boivin K, Acarkan A, Mbulu R S, et al. The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes[J]. Plant Physiol., 2004, 135(8): 735～744.
[97] Kuittinen H, Haan D, Vogl A A, et al. Comparing the linkage maps of the close relatives Arabidopsis lyrata and Arabidopsis thaliana[J]. Genetics, 2004, 168(3): 1575～1584.
[98] Marcus A K, Markus K. genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species capsella rubella, Arabidopsis lyrata subsp. petraea, and a. thaliana[J]. American Journal of Botany, 2005, 92(4): 761～767.
[99] Warwick S I, Black L D. Molecular phylogenies from theory to application in Brassica and allies (tribe Brassiceae, Brassicaceae)[J]. Opera Bot., 1997, 132(5): 159～168.
[100] Lysak M A, Koch M A, Pecinka A, et al. Chromosome triplication found across the tribe Brassiceae[J]. Genome Res., 2005, 15(9): 516～525.
[101] Christopher D T, Cheung F, Maiti R, et al. Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy[J]. The PlantCell, 2006, 18(6): 1348～1359.
[102] Yang T J, Kim J S, Kwon S J, et al. Sequence Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa[J]. The Plant Cell, 2006, 18(6): 1339～1347.
[103] Yang Y W, Lai K N, Tai P Y, et al. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages[J]. J. Mol. Evol., 1999, 48(5): 597～604.
[104] Zhang M Q. Computational prediction of eukaryotic protein coding genes[J]. Nature, 2002, 3(9): 698～709.
[105] Salamov A, Solovyev V. An initio gene finding in Drosophila genomic DNA[J]. Genome Res., 2000, 10(4): 516～522.
[106] Burge C, Karlin S. Prediction of complete gene structure in human genomic DNA[J]. Journal of Molecular Biology, 1997, 268(12): 78～94.
[107] Lomsadze A, Terhovhannisyan V, Chernoff Y, et al. Gene identification in novel eukaryotic genomes by self-training algorithm[J]. Nucl. Acid. Res., 2005, 33(20): 6494～6506.
[108] Kulp D, Haussler D, Reese M G, et al. A generalized hidden Markov model for the recognition of human genes in DNA[J]. Intell. Syst. Mol. Biol., 1996, 4: 134～142.
[109] Solovyev V, Salamov V A A, Lawrence C B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames[J]. Nucl. Acid. Res., 1994, 22(24): 5156～5163.
[110] Borodovsky M, McIninch J. GENMARK: parallel gene recognition for both DNA strands[J]. Comp. Chem., 1993, 17(7): 123～133.
[111] Parsons J D. Miropeats: graphical DNA sequence comparisons[J]. Comput. Appl. Biosci., 1995, 11(6): 615～619.
[112] Kurtz S, Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes[J]. Bioinformatics, 1999, 15(5): 426～427. Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high density picolitre reactors[J]. Nature, 2005, 437(7057): 376～380.
[113] Lander E S, Linton L M, Birren B, et al. Initial sequencing and analysis of the human genome[J]. Nature, 2001, 409(6822): 860～921.
[114] Gaut B S, Doebley J F. DNA sequence evidence for the segmental allopolyploid origin of maize[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(5): 6808～6814.
[115] Shoemaker R C, Polzin K, Labate J, et al. Gemome duplication in soybean(Glycine subgenus soja)[J]. Genetics, 1996, 144(13): 329～338.
[116] Lagercrantz U, Lydiate D. Comparative genome mapping in Brassica[J]. Genetics, 1996, 144(4): 1903～l9l0.
[117] Tian C G, Xiong Y Q, Liu T Y, et al. Evidence for an ancient whole genome duplication event in rice and other cereals[J]. Chin. J. Genet., 2005, 32(5): 519～527.
[118] Kellogg E A. Relationships of cereal crops and other grasses[J]. Proc. Nati. Acad. Sci. USA, 1998, 95(5): 2005～2010.
[119] Kellogg E A. The grasses: a case study in macroevolution[J]. Annu. Rev. Ecol. Syst., 2000, 31(9):217～238.
[120] Gilbert W. Why genes in pieces[J]. Nature, 1978, 271(5645): 501.
[121] Patthy L. Exon shuffling and other ways of module exchange[J]. Matrix Biol., 1996, 15(5): 301～312.
[122] Rijk V A, Bloemendal H. Molecular mechanisms of exon shuffling: illegitimate recombination[J]. Genetica, 2003, 118(2-3): 245～249.
[123] Rijk V A, Jong W, Bloemendal H. Exon shuffling mimicked in cell culture[J]. Proc. Nati. Acad. Sci. USA, 1999, 96(14): 8074～8079.
[124] Moran J, DeBerardinis V, Kazazian R J, et al. Exon shuffling by L1 retrotransposition[J]. Science, 1999, 283(5407): 1530～1534.
[125] Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes[J]. Nature Genet., 2000, 24(4): 363～367.
[126] Kaessmann H, Zollner S, Nekrutenko A, et al. Signatures of domain shuffling in the human genome[J]. Genome Res., 2002, 12(11): 1642～1650.
[127] Souza S J, Long M, Schoenbach L, et al. Intron positions correlate with module boundaries in ancient proteins[J]. Proc. Nati. Acad. Sci. USA, 1996, 93(25): 14632～14636.
[128] Ohno S. Evolution by Gene Duplication[M]. Berlin: Springer, 1970.
[129] Kimura M. The Neutral Theory of Molecular Evolution[M]. Cambridge: Cambridge Univ. Press, 1983.
[130] Prince V E, Pickett F B. Splitting pairs: the diverging fates of duplicated genes[J]. Nature Rev. Genet., 2002, 3(11): 827～837.
[131] Bailey J A, Gu Z, Clark R A, et al. Recent segmental duplications in the human genome[J]. Science, 2002, 297(5583): 1003～1007.
[132] Samonte R V, Eichler E E. Segmental duplications and the evolution of the primate genome[J]. Nature Rev. Genet., 2002, 3(1): 65～72.
[133] Wang W, Brunet F G, Nevo E, et al. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster[J]. Proc. Nati. Acad. Sci. USA, 2002, 99(7): 4448～4453.
[134] Betrán E, Wang W, Jin L, et al. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene[J]. Mol. Biol. Evol. ,2002, 19(5): 654～663.
[135] Betrán E, Long M. Expansion of genome coding regions by acquisition of new genes[J]. Genetica , 2002, 115(1): 65～80.
[136] Pickeral O K, Makalowski W, Boguski M S, et al. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition[J]. Genome Res., 2000, 10(4): 411～415.
[137] Makalowski W, Mitchell G A, Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability[J]. Trends Genet, 1994, 10(6): 188～193.
[138] Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein coding genes[J]. Trends Genet., 2001, 17(6): 619～621.
[139] Sorek R, Ast G, Graur D. Alu containing exons are alternatively spliced[J]. Genome Res., 2002, 12(7): 1060～1067.
[140] Makalowski W. Genomic scrap yard: how genomes utilize all that junk[J]. Gene, 2000, 259(15):61～67.
[141] Lorenc A, Makalowski W. Transposable elements and vertebrate protein diversity[J]. Genetica, 2003, 118(2-3): 183～191.
[142] Ochman H. Lateral and oblique gene transfer[J]. Curr. Opin. Genet. Dev., 2001, 11(6): 616～619.
[143] De Koning A P, Brinkman F S, Jones S J, et al. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis[J]. Mol. Biol. Evol., 2000, 17(11): 1769～1773.
[144] Bergthorsson U, Adams K L, Thomason B, et al. Widespread horizontal transfer of mitochondrial genes in flowering plants[J]. Nature, 2003, 424(6945): 197～201.
[145] Thomson T M, Lozano J J, Loukili N, et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene[J]. Genome Res., 2000, 10(11): 1743～1756.
[146] Ranz J M, Ponce A R, Hartl D L, et al. Origin and evolution of a new gene expressed in the Drosophila sperm axoneme[J]. Genetica, 2003, 118(2-3): 233～244.
[147] McCarthy A D, Hardie D G. Fatty acid synthase an example of protein evolution by gene fusion[J]. Trends Biochem. Sci., 1984, 4(5): 60～63.
[148] Snel B, Bork P, Huynen M. Gene fusion versus gene fission[J]. Trends Genet., 2000 16(1): 9～11.
[149] Nurminsky D I, Nurminskaya M V, De Aguiar D, et al. Selective sweep of a newly evolved sperm specific gene in Drosophila[J]. Nature, 1998, 396(6711): 572～575.
[150] Chen L, DeVries A L, Cheng C H. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(8): 3817～3822.
[151] Chen L, DeVries A L, Cheng C H. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish[J]. Proc. Nati. Acad. Sci. USA, 1997, 94(8): 3811～3816.
[152] Martignetti J A, Brosius J. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(6): 9698～9702.
[153] Martignetti J A, Brosius J. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element[J]. Proc. Nati. Acad. Sci. USA, 1993, 90(24): 11563～11567.
[154] Long M, Langley C H. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila[J]. Science, 1993, 260(5104): 91～95.
[155] Begun D J. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila[J]. Genetics, 1997, 145(2): 375～382.
[156] Malik H S, Henikoff S. Adaptive evolution of Cid, a centromere specific histone in Drosophila[J]. Genetics, 2001, 157(3): 1293～1298.
[157] Betrán E, Long M. Dntf-2r: a young Drosophila retroposed gene with specific male expression under positive Darwinian selection[J]. Genetics, 2003, 164(3): 977～988.
[158] Zhang J, Zhang Y P, Rosenberg H F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey[J]. Nat. Genet., 2002, 30(4): 411～415.
[159] Zhang J, Webb D M, Podlaha O. Accelerated protein evolution and origins of human specific features: Foxp2 as an example[J]. Genetics, 2002, 162(4): 1825～1835.
[160] Enard W, Przeworski M, Fisher S E, et al. Molecular evolution of FOXP2, a gene involved in speech and language[J]. Nature, 2002, 418(6900): 869～872.
[161] Courseaux A, Nahon J L. Birth of two chimeric genes in the Hominidae lineage[J]. Science, 2001, 291(5507): 1293～1297.
[162] Johnson M E, Viggiano L, Bailey J A, et al. Positive selection of a gene family during the emergence of humans and African apes[J]. Nature, 2001, 413(6855): 514～519.
[163] Paulding C A, Ruvolo M, Haber D A. The Tre2 (USP6) oncogene is a hominoid specific gene[J]. Proc. Nati. Acad. Sci. USA, 2003, 100(8): 2507～2511.
[164] Javaud C, Dupuy F, Maftah A, et al. The fucosyltransferase gene family: an amazing summary of the underlying mechanisms of gene evolution[J]. Genetica, 2003, 118(2-3): 157～170.
[165] Maston G A, Ruvolo M. Chorionic gonadotropin has a recent origin within primates and an evolutionary history of selection[J]. Mol. Biol. Evol., 2002, 19(9): 320～335.
[166] Brosius J. The contribution of RNAs and retroposition to evolutionary novelties[J]. Genetica, 2003, 118(2-3): 99～116.
[167] Brosius J, Gould S J. On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA”[J]. Proc. Nati. Acad. Sci. USA, 1992, 89(22): 10706～10710.
[168] Gogolevskaya I K, Kramerov D A. Evolutionary history of 4.5SI RNA and indication that it is functional[J]. J. Mol. Evol., 2002, 54(3): 354～364.
[169] Long M, De Souza S J, Rosenberg C, et al. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor[J]. Proc. Nati. Acad. Sci. USA, 1996, 93(15): 7727～7731.
[170] Majoros W H, Pertea M, Antonescu C, et al. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders[J]. Nucl. Acid. Res., 2003, 31(13): 3601～3604.
[171] Leutwiler L S, Hough E B R, Meyerowitz E M. The DNA of Arabidopsis thaliana[J]. Mol. Gen. Genet., 1984, 194(6): 15～23.
[172] Flavell R. Repetitive DNA and chromosome evolution in plants[J]. Philos. Trans. R. Soc. Lond. B., 1986, 312(1154): 227～242.
[173] Takashi M, Wu J Z, Hiroyuki K, et al. The map-based sequence of the rice genome[J]. Nature, 2005, 436(7052): 793～800.
[174] Yu J, Hu S N, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica)[J]. Science, 2002, 296(5565): 79～92.
[175] Goff S A, Ricke D, Lan T H, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)[J]. Science, 2002, 296(5565): 92～100.
[176] Sasaki T, Matsumoto T, Yamamoto K, et al. The genome sequence and structure of rice chromosome 1[J]. Nature, 2002, 420(6913): 312～316.
[177] Pertea M, Salzberg S L. Computational gene finding in plants[J]. Plant Mo1. Bio1., 2002, 48(1-2): 39～48.
[178] Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4[J]. Nature, 2002, 420(6913): 316～320.
[179] SanMiguel P J, Ramakrishna W, Bennetzen J L, et al. Transposable elements, genes and recombination in a 215kb contig from wheat chromosome 5A(m)[J]. Funct. Integr. Genomics, 2002, 2(1-2): 70～80.
[180] Nathalie P, Stephane R, Patrice D, et al. Evaluation of gene prediction software using a genomicdata set: application to Arabidopsis thaliana sequences[J]. Bioinformatics, 1999, 15(7): 887～899.
[181] Burset M, Guigo R. Evaluation of Gene Structure Prediction Programs[J]. Genomics, 1996, 34(3): 353～367.
[182] Salzberg S L, Delcher A L, Kasif S, et al. Microbial gene identification using interpolated Markov models[J]. Nucl. Acid. Res., 1998, 26(5): 544～548.
[183] Werner T. Models for prediction and recognition of eukaryotic promoters[J]. Mamm. Genome, 1999, 10(2): 168～175.
[184] Masterson J. Stomatal size in fossil plants: Evidence for polyploid in majority of angiosperms[J]. Science, 1994, 264(5146): 421～424.
[185] Lee H S, Chen Z J. Protein coding genes are epigenetically regulated in Arabidopsis polyploids[J]. Proc. Nati. Acad. Sci. USA, 2001, 98(12): 6753～6758.
[186] Kashkush K, Feldman M, Levy A A. Gene loss, silencing and activation in newly synthesized wheat allopolyploid[J]. Genetics, 2002, 160(4): 1651～1659.
[187] Adams K L, Percifield R, Wendek J F. Organ specific silencing of duplicated genes in a newly synthesized cotton allotetraploid[J]. Genetics, 2004, 168(4): 2217～2226.
[188] Comai L, Tyagi A P, Winter K, et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids[J]. Plant Cell, 2000, 12(9): 1551～1568.
[189] Kashkush K, Feldman M, Levy A A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat[J]. Nat. Genet., 2003, 33(1): 102～106.
[190] He P, Friebe B R, Gill B S, et al. Allopolyploidy alters gene expression in the highly stable hexaploid wheat[J]. Plant Mo1. Bio1., 2003, 52(2): 401～4l4.