Buell C Robin, Yuan Qiaoping, Ouyang Shu, Liu Jia, Zhu Wei, Wang Aihui, Maiti Rama, Haas Brian, Wortman Jennifer, Pertea Mihaela, Jones Kristine M, Kim Mary, Overton Larry, Tsitrin Tamara, Fadrosh Douglas, Bera Jayati, Weaver Bruce, Jin Shaohua, Johri Shivani, Reardon Matt, Webb Kristen, Hill Jessica, Moffat Kelly, Tallon Luke, Van Aken Susan, Lewis Matthew, Utterback Teresa, Feldblyum Tamara, Zismann Victoria, Iobst Stacey, Hsiao Joseph, de Vazeille Aymeric R, Salzberg Steven L, White Owen, Fraser Claire, Yu Yeisoo, Kim HeyRan, Rambo Teri, Currie Jennifer, Collura Kristi, Kernodle-Thompson Shelly, Wei Fusheng, Kudrna Kudrna, Ammiraju Jetty Siva S, Luo Meizhong, Goicoechea Jose Luis, Wing Rod A, Henry David, Oates Ryan, Palmer Michael, Pries Gina, Saski Christopher, Simmons Jessica, Soderlund Carol, Nelson William, de la Bastide Melissa, Spiegel Lori, Nascimento Lidia, Huang Emily, Preston Raymond, Zutavern Theresa, Palmer Lance, O'Shaughnessy Andrew, Dike Sujit, McCombie W Richard, Minx Pat, Cordum Holly, Wilson Richard, Jin Weiwei, Lee Hye-Ran, Jiang Jiming, Jackson Scott
The Institute for Genomic Research, Rockville, Maryland 20850, USA.
Genome Res. 2005 Sep;15(9):1284-91. doi: 10.1101/gr.3869505. Epub 2005 Aug 18.
Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
水稻（Oryza sativa L.）的3号染色体在栽培谷物中具有进化保守性，并且与玉米和高粱共享大片的同线性区域，玉米和高粱在5000多万年前与水稻分化。为了全面了解这条染色体，我们对粳稻品种日本晴的36.1 Mb（约97%）进行了测序、完成组装并注释。该染色体的注释特征包括5915个基因，其中913个与转座元件相关。可以为3064个基因赋予推定功能，另有757个基因被注释为表达基因，剩下2094个基因编码假定蛋白。与拟南芥蛋白质组的相似性搜索揭示了3号染色体上67%的蛋白质的推定同源物。进一步搜索非冗余氨基酸数据库、Pfam结构域数据库、植物表达序列标签以及高粱和玉米的基因组组装序列，发现3号染色体上只有853个与转座元件无关的蛋白质与其他已知序列缺乏相似性。有趣的是，其中426个在水稻基因组中有旁系同源物。野生祖先物种尼瓦拉野生稻与粳稻3号染色体的比较物理图谱显示这两个物种之间具有高度的序列同一性和同线性，它们大约在1万年前分化。虽然未检测到重大重排，但尼瓦拉野生稻3号染色体的推断大小比粳稻小21%。利用整合的玉米物理图谱和小麦遗传图谱进行水稻与其他谷物之间的同线性分析，结果显示同线性程度非常高，这进一步支持将水稻，特别是3号染色体，用作谷物间比较研究的模型。
