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水稻基因组进化的新见解:高度的基因共线性和逆转座子扩增差异

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification.

作者信息

Zhang Shibo, Gu Yong Qiang, Singh Jaswinder, Coleman-Derr Devin, Brar Darshan S, Jiang Ning, Lemaux Peggy G

机构信息

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

出版信息

Plant Mol Biol. 2007 Jul;64(5):589-600. doi: 10.1007/s11103-007-9178-3. Epub 2007 May 30.

DOI:10.1007/s11103-007-9178-3
PMID:17534720
Abstract

An approximately 247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous approximately 450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged approximately 10 million years ago. Comparisons of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated rice.

摘要

将来自野生稻短药野生稻(Oryza brachyantha)FF基因组的大约247 kb基因组区域(其拥有最小的稻属基因组)与来自AA基因组的亚洲栽培稻(O. sativa L. ssp. japonica)的直系同源大约450 kb区域进行了比较。直系同源区域中的38个基因中有37个在粳稻和短药野生稻之间共享。编码区核苷酸替代分析表明,这两个基因组大约在1000万年前发生了分化。转座元件(TEs)的比较显示,短药野生稻中DNA转座元件的密度与亚洲栽培稻相当;然而,RNA转座元件的密度则显著更低。粳稻中RNA转座元件的基因组比例比短药野生稻大两倍。该区域以及来自五个野生和两个栽培稻种的BAC末端序列中的差异,特别是RNA转座元件方面的差异,解释了栽培稻和短药野生稻之间主要的基因组大小差异。对测序区域中三个ObDREB1基因的基因表达分析表明,直系同源基因在冷胁迫后保留相似的表达模式。我们的结果表明,RNA转座元件的大小和数量在稻属的基因组分化和进化中起主要作用。此外,亲缘关系较远的短药野生稻与亚洲栽培稻具有共线性,这为利用比较基因组学探索野生物种的遗传多样性以改良栽培稻提供了机会。

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