Curated genome annotation of Oryza sativa ssp japonica and comparative genome analysis with Arabidopsis thaliana -: The Rice Annotation Project
Curated genome annotation of Oryza sativa ssp japonica and comparative genome analysis with Arabidopsis thaliana -: The Rice Annotation Project
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DOI：
10.1101/gr.5509507
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发表时间：
2007-02-01
期刊：
影响因子：
7
通讯作者：
Gojobori, Takashi
中科院分区：
文献类型：
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作者：
Gojobori, Takashi
本文报道了水稻（Oryza sativa L. ssp）全基因组的注释。日本粳稻品种。所有蛋白质和非蛋白质编码RNA （npRNA）候选物的功能注释都是手工整理的。鉴定或推断出19,969个（70%）蛋白的功能，并发现131个可能的nprna（包括58个反义转录物）。在插入突变系中发现了近5000个注释的蛋白质编码基因被破坏，这将加速未来对注释的实验验证。利用从水稻和其他代表性谷物中获得的cDNA序列来确定水稻位点。我们基于这些位点的保守估计和外推表明，水稻的基因数量接近32,000，这比以前的估计要小。我们对水稻和拟南芥进行了比较分析，发现两个基因组都具有几个谱系特异性基因，这可能解释了这些物种之间观察到的差异，而它们在蛋白质序列中具有相似的预测功能域。控制翻译效率的系统似乎在大的进化距离中是保守的。此外，还研究了蛋白质编码基因的进化过程。我们的研究结果表明，自然选择可能在两个物种的复制基因中发挥了作用，因此复制以一种依赖于基因功能的方式被抑制或偏爱。
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is similar to 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.