The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle
The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle
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DOI：
10.1534/genetics.112.148809
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发表时间：
2013-04-01
期刊：
影响因子：
3.3
通讯作者：
Sternberg, Paul W.
中科院分区：
文献类型：
--
作者：
Srinivasan, Jagan;Dillman, Adler R.;Sternberg, Paul W.
线虫是一个丰富多样的无脊椎动物门，其成员几乎栖息于每一个生态位。再vipanagrellus（“微虫”）是一种自由生活的线虫，由于其与秀丽隐杆线虫的系统发育距离，经常被用来了解发育和行为过程的进化。在这里，我们报告了再病毒的基因组、转录组和小rna的从头测序。使用自动基因查找器和RNA-seq数据的组合，我们预测了24,249个基因和32,676个转录本。小RNA分析发现248个microRNA （miRNA）发夹，其中63个在其他物种中有同源物。共发现包含42个miRNA前体的14个miRNA簇。RNA干扰、细胞发育和程序性细胞死亡途径在很大程度上是保守的。蛋白质家族结构域丰度分析显示，再病毒疟原虫经历了BTB结构域蛋白的显著扩增和cullin支架蛋白家族的前所未有的扩增，cullin支架蛋白家族涉及多亚基泛素连接酶，这表明蛋白质水解可塑性和/或更严格的蛋白质周转调节。真核释放因子蛋白家族也急剧扩大，表明与病毒和转座子的进化军备竞赛正在进行。再病毒疟原虫的基因组提供了一个资源，以推进我们对线虫进化和生物学的理解，并进一步阐明导致自由生活谱系的基因组结构，利用这种蠕虫的许多迷人的特征，通过比较研究揭示。
Nematodes compose an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the "microworm") is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA-seq data, we predict 24,249 genes and 32,676 transcripts. Small RNA analysis revealed 248 microRNA (miRNA) hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. The RNA interference, dauer development, and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain-containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi-subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.