Genome-Wide Survey and Comparative Analysis of LTR Retrotransposons and Their Captured Genes in Rice and Sorghum

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.

长末端重复序列（Long Terminal Repeat, LTR）反转录转座子是植物中主要的第一类移动遗传元件。它们在基因扩张、物种多样化及进化过程中发挥关键作用。尽管多数植物基因组已完成全序列测定，但在大多数植物中，这类元件所捕获的基因仍未实现全基因组范围的鉴定与特征分析。本研究分别在水稻和高粱基因组中鉴定到7043个和23915个全长LTR反转录转座子。水稻全长LTR反转录转座子有较高比例分布于各染色体的着丝粒区域附近；与之相反，高粱全长LTR反转录转座子并未在着丝粒区域富集。这种分布差异可能源于二者从共同祖先分化后反转录转座过程的差异，进而可能推动了物种分化。上述两类元件分别在水稻和高粱基因组中共捕获了672个和1343个基因。基因本体论（Gene Ontology, GO）及基因集富集分析（Gene Set Enrichment Analysis, GSEA）结果显示，水稻LTR捕获基因中未发现显著富集的GO术语；而高粱LTR捕获基因则富集了参与DNA/RNA代谢及染色质组织的GO功能术语。仅36%的水稻LTR捕获基因存在表达现象，其表达分化率经估算为11.9%。较高比例的水稻LTR捕获基因在中性选择压力下进化为假基因。与之相反，高粱LTR捕获基因中有更高比例处于净化选择压力之下，且其中72.4%的基因存在表达，因此更多高粱LTR捕获基因仍具备功能。小RNA分析结果表明，水稻和高粱中的部分LTR捕获基因可能参与负调控过程。此外，水稻和高粱的LTR捕获基因均受到正选择作用，其中部分基因仍可表达并具备功能。上述数据提示，部分LTR捕获基因可能已演化出全新的基因功能。