Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.
Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.
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DOI：
10.1371/journal.pone.0071118
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Ramachandran S
中科院分区：
文献类型：
--
作者：
Jiang SY;Ramachandran S
长末端重复序列(LTR)反转录转座子是植物中主要的I类活动元件。它们在基因扩张、多样化和进化中发挥着关键作用。然而，尽管许多基因组已经完全测序，但它们捕获的基因在大多数植物中还没有得到基因组广泛的鉴定和特征。在本研究中，我们在水稻和高粱基因组中分别鉴定了7,043个和23,915个全长LTR反转录转座子。水稻全长LTR反转录转座子在每条染色体的着丝粒区附近分布比例较高。相反，高粱全长LTR反转录转座子没有在着丝粒区域富含。这种不同可能是由于在分化过程中和分化后与其共同祖先的逆转座不同，因此可能是导致物种分化的原因。这些元素分别在水稻和高粱中捕获了672个和1343个基因。基因本体论(GO)和基因集浓缩分析(GSEA)表明，在获得的水稻基因中没有发现GO术语的过度表达。对于LTR捕获的高粱基因，GO在DNA/RNA代谢和染色质组织中的功能被过度表达。只有36%的水稻基因获得了表达，表达差异估计为11.9%。在中性选择条件下，获得的水稻基因中有较高比例进化为假基因。相反，获得的高粱基因中有较高比例的基因处于纯化选择状态，其中72.4%得到了表达。因此，较高比例的LTR捕获的高粱基因是有功能的。小RNA分析表明，在水稻和高粱中捕获的一些LTR基因可能参与了负调控。另一方面，在水稻和高粱中都观察到了正选择，其中一些基因仍然具有表达和功能。这些数据表明，这些LTR捕获的基因中的一些可能已经进化成新的基因功能。
Long terminal repeat (LTR) retrotransposons are the major class I mobile elements in plants. They play crucial roles in gene expansion, diversification and evolution. However, their captured genes are yet to be genome-widely identified and characterized in most of plants although many genomes have been completely sequenced. In this study, we have identified 7,043 and 23,915 full-length LTR retrotransposons in the rice and sorghum genomes, respectively. High percentages of rice full-length LTR retrotransposons were distributed near centromeric region in each of the chromosomes. In contrast, sorghum full-length LTR retrotransposons were not enriched in centromere regions. This dissimilarity could be due to the discrepant retrotransposition during and after divergence from their common ancestor thus might be contributing to species divergence. A total of 672 and 1,343 genes have been captured by these elements in rice and sorghum, respectively. Gene Ontology (GO) and gene set enrichment analysis (GSEA) showed that no over-represented GO term was identified in LTR captured rice genes. For LTR captured sorghum genes, GO terms with functions in DNA/RNA metabolism and chromatin organization were over-represented. Only 36% of LTR captured rice genes were expressed and expression divergence was estimated as 11.9%. Higher percentage of LTR captured rice genes have evolved into pseudogenes under neutral selection. On the contrary, higher percentage of LTR captured sorghum genes were under purifying selection and 72.4% of them were expressed. Thus, higher percentage of LTR captured sorghum genes was functional. Small RNA analysis suggested that some of LTR captured genes in rice and sorghum might have been involved in negative regulation. On the other hand, positive selection has been observed in both rice and sorghum LTR captured genes and some of them were still expressed and functional. The data suggest that some of these LTR captured genes might have evolved into new gene functions.
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