Identification and characterization of lineage-specific genes within the Poaceae
Identification and characterization of lineage-specific genes within the Poaceae
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DOI：
10.1104/pp.107.104513
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发表时间：
2007-12-01
期刊：
影响因子：
7.4
通讯作者：
Buell, C. Robin
中科院分区：
文献类型：
--
作者：
Campbell, Matthew A.;Zhu, Wei;Buell, C. Robin
利用水稻（Oryza sativa）sp. japonica基因组注释，沿着来自植物界184个物种的基因组序列和聚类转录本组装，我们已经确定了一组861个水稻基因，这些基因在禾本科6个不同物种中进化保守，但与禾本科以外的植物物种缺乏显着的序列相似性。这组进化上保守的和谱系特异性的水稻基因被称为保守的禾本科特异性基因（CPSGs），以反映在三个独立的禾本科亚科之间存在显着的序列相似性。绝大多数水稻CPSG（86.6%）编码的蛋白质没有推定的功能或功能特征的蛋白质结构域。对于其余的CPSG，8.8%编码含有F-box结构域的蛋白，4.5%编码具有推定功能的蛋白。此外，CPSG具有更少的外显子，更短的总基因长度，和highatedGC含量相比，注释为转座因子（TE）或那些基因具有显着的序列相似性，在一个物种以外的禾本科。CPSG与其他禾本科物种的序列的多个序列比对显示跨推定结构域、新结构域或蛋白质的整个编码长度的保守性。在基因组水平上，高粱（两色高粱）和861个水稻CPSG中的103个（12.0%）可以进行同线比对，表明这组基因在禾本科内具有额外的保守性。广泛的序列相似性，在进化上不同的物种在禾本科家庭和一个额外的屏幕TE相关的结构特征和序列折扣这些CPSG被错误注释的TE。总的来说，这些数据证实，我们已经确定了一组特定的基因是高度保守的，以及具体的，禾本科。
Using the rice ( Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function or functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain-containing protein and 4.5% encode a protein with a putative function. Onaverage, the CPSGs have fewer exons, shorter total gene length, and elevatedGC content when compared with genes annotated as either transposable elements (TEs) or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum ( Sorghum bicolor) and 103 of the 861 rice CPSGs (12.0%) could be made, demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for TE-related structural characteristics and sequence discounts these CPSGs as being misannotated TEs. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae.