Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
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DOI：
10.1104/pp.109.139402
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发表时间：
2009-08-01
期刊：
影响因子：
7.4
通讯作者：
Ramachandran, Srinivasan
中科院分区：
文献类型：
--
作者：
Jiang, Shu-Ye;Christoffels, Alan;Ramachandran, Srinivasan
在每个完全测序的基因组中，30%到50%的基因被注释为未表征的假设基因。在水稻基因组中，10,918个假设基因在密歇根州立大学水稻基因组注释的最新版本(版本6)中被注释。我们采用了一种综合的方法来分析它们的复制/扩展和功能。分析表明，串联/片段复制和转座/反转座显著促进了假设基因的扩展，尽管它们的贡献率不同。从逆转录基因、串联基因、节段性基因、打包基因或长终止的与直接重复相关的复制/扩展中总共检测到3769个假设基因。每位点非同义替换和每位点同义替换分析表明，其中21.65%的基因仍具有功能，占假设基因总数的7.47%。全球表达分析已经确定了1,672个表达的假设基因。其中，415个基因可能以发育阶段特异的方式发挥作用。反义链表达和小RNA分析表明，这些假说基因中有很高比例可能在负调控基因表达方面发挥重要作用。对拟南芥、玉米、高粱和籼稻基因组的同源搜索表明，大多数假设基因都可以从最近进化的基因组序列中注释出来。这些数据促进了对水稻假想基因的理解，这些基因参与了特定谱系的扩展，并在特定的发育阶段发挥功能。我们的分析还为其他生物中假想基因的表征和功能注释提供了有价值的手段。
In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.