植物LTR-反转座子中Orf1基因的分子进化
收稿日期: 2013-04-22
修回日期: 2013-05-22
网络出版日期: 2013-09-25
基金资助
国家人社部留学回国人员启动基金项目(编号：人社厅函[2012]258号), 江苏省六大人才高峰项目(编号：2011NY030), 中国农科院棉花所棉花生物学国家重点实验室开放课题项目(编号：CB2013B06)和江苏省农业科技自主创新基金项目(编号：CX(12)5036)资助
Molecular evolution of Orf1 gene in plant LTR-retrotransposons
Received date: 2013-04-22
Revised date: 2013-05-22
Online published: 2013-09-25
LTR-反转座子是植物基因组的主要组成部分。它们在结构上非常保守, 通常含有gag和pol两个基因, 是完成其转座过程所必需的。在前期研究中, 本项目组对大豆基因组SARE转座子家族进行了详细的分析。结果表明, 该家族的拷贝中还存在第3个基因——Orf1。文章借助生物信息学的研究方法, 对33个已测序的基因组进行了全基因组注释。结果发现, 在7个植物基因组(桉树、杨树、棉花、大豆、百脉根、亚麻和苜蓿)中, 部分LTR-反转座子元件在gag基因的上游存在约1~2 kb未知的Orf1基因或基因片段。这类转座子多数在0~3百万年内插入到其所在的寄主基因组中, 但它们在不同物种中的分子结构、发生的频率、扩增的强度和活跃的时期等方面差异较大。系统进化树分析表明, 这类具有特殊结构的转座子较整齐的聚类到双子叶植物的一个进化分支上, 表明它们可能是部分双子叶植物在进化过程中所产生的。不同物种间的相对保守性、大量拷贝的转录活性以及可能存在的多个功能结构域, 提示Orf1基因可能具有一定的生物学功能。
刘静 杜建厂 . 植物LTR-反转座子中Orf1基因的分子进化[J]. 遗传, 2013 , 35(9) : 1117 -1124 . DOI: 10.3724/SP.J.1005.2013.01117
LTR-Retrotransposons are the major DNA components in plant genomes. They usually contain gag and pol, two genes necessary for transpositinal process. Our previous study on soybean genome annotation identified a SARE LTR-Retrotransposon family, which carries the third gene, Orf1.Using a bioinformatics approach, we here reported that 7 out of 33 sequenced genomes have some LTR-Retrotransposons with an extra Orf1 gene/gene fragment (~1-2 kb) in the region between 5′ LTR and gag gene, including Eucalyptus grandis, Populus trichocarpa, Gossypium raimondii, Glycine max, Lotus japonica, Linum usitatissimum, and Medicago truncatula. The majority of these elements were inserted into the genomes they reside within the last 3 million years, but their structures, frequencies, intensity, and activity in different host genomes are quite different. Phylogenetic analysis indicated that these unusual elements were clustered in a eudicot branch, suggesting that they may be generated in the evolution of some eudicot species. The relative conservation, transcriptional activity, and the presence of multiple potential conserved motifs suggest that Orf1 gene may still be functional.
Key words： plant genomes; LTR-retrotransposons; origin; evolution; Orf1 gene
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