Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features.
Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features.
复制标题
线虫中基于 RNA 的基因重复的进化模式与其基因组特征一致
DOI：
10.1186/1756-0500-5-398
复制
发表时间：
2012-08-01
影响因子：
1.8
通讯作者：
He S
中科院分区：
文献类型：
--
作者：
Zou M;Wang G;He S
背景
基于RNA的基因复制（逆转录）在许多生理过程中发挥着关键作用。目前，在哺乳动物、果蝇、植物、斑马鱼等脊索动物中已发现了功能性逆转录复制，但在小杆线虫中的研究尚未见报道。
结果
我们在C中鉴定了43、48、43、9和42个逆转录拷贝，其中6、15、18、3和13个形成嵌合基因。brenneri，C.布里格塞角elegans、秀丽隐杆线虫C. japonica和C. remanei，分别。小杆线虫至少存在5种嵌合体类型，其中最常见的是N端和C端同时参与的逆转录。不同的分析证据表明，许多逆转录和几乎所有的嵌合基因可能在这些物种中的功能。大约一半的retrocopies在每个物种的坐标在其他物种，我们建议，retrocopies在密切相关的物种可能有助于确定retrocopies为某个物种。
结论
小杆线虫基因组中存在大量逆转录基因和嵌合基因，其中一些可能具有功能。这些基因的进化模式可能与它们的基因组特征有关，如逆转录因子的活性、高突变率和缺失率以及大比例的基因进行反式剪接。
Background
RNA-based gene duplicates (retrocopies) played pivotal roles in many physiological processes. Nowadays, functional retrocopies have been systematically identified in several mammals, fruit flies, plants, zebrafish and other chordates, etc. However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported.
Findings
We identified 43, 48, 43, 9, and 42 retrocopies, of which 6, 15, 18, 3, and 13 formed chimeric genes in C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. At least 5 chimeric types exist in Caenorhabditis species, of which retrocopy recruiting both N and C terminus is the commonest one. Evidences from different analyses demonstrate many retrocopies and almost all chimeric genes may be functional in these species. About half of retrocopies in each species has coordinates in other species, and we suggest that retrocopies in closely related species may be helpful in identifying retrocopies for one certain species.
Conclusions
A number of retrocopies and chimeric genes exist in Caenorhabditis genomes, and some of them may be functional. The evolutionary patterns of these genes may correlate with their genomic features, such as the activity of retroelements, the high rate of mutation and deletion rate, and a large proportion of genes subject to trans-splicing.