Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica
Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica
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DOI：
10.1093/molbev/msh207
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发表时间：
2004-11-01
影响因子：
10.7
通讯作者：
Chourrout, D
中科院分区：
文献类型：
--
作者：
Volff, JN;Lehrach, H;Chourrout, D
逆转录转座因子在真核生物DNA的形成中起着重要作用，其活性和周转率直接影响基因组的大小。在65-75兆碱基范围内有大约15，000个基因，海洋被囊动物Oikopleura dioica，一种非脊椎脊索动物，具有动物中发现的最小和最紧凑的基因组。与大量消除逆转录元件一致，在41兆碱基的非冗余基因组序列中只检测到一个明显新颖的非长末端重复（非LTR）逆转录转座子分支。相比之下，在被囊玻璃海鞘的不太紧凑的基因组中鉴定出至少六个非LTR元件的进化枝。出乎意料的是，Ty 3/gypsy相关的Tor LTR反转录转座子在O. dioica。它们通常很差或显然没有损坏，表明最近的活动。Tor 3和Tor 4 b家族均具有类似于牛的开放阅读框架，表明可能通过感染水平获得。Tor 4 b病毒样基因可能来自副粘病毒（RNA病毒）。Tor 3和Tor 4 b在遗传学上明显不同于脊椎动物逆转录病毒（逆转录病毒科），并且更容易让人联想到某些昆虫和植物序列。Tor元件可能代表了一种迄今未知的、古老的脊索动物感染性逆转录酶。它们在被囊动物和其他脊索动物中的分布和传播动态值得进一步研究。
Retrotransposable elements have played an important role in shaping eukaryotic DNA, and their activity and turnover rate directly influence the size of genomes. With approximately 15,000 genes within 65-75 megabases, the marine tunicate Oikopleura dioica, a nonvertebrate chordate, has the smallest and most compact genome ever found in animals. Consistent with a massive elimination of retroelements, only one apparently novel clade of non-long terminal repeat (non-LTR) retrotransposons was detected within 41 megabases of nonredundant genomic sequences. In contrast, at least six clades of non-LTR elements were identified in the less compact genome of the tunicate Ciona intestinalis. Unexpectedly, Ty3/gypsy-related Tor LTR retrotransposons presented an astonishing level of diversity in O. dioica. They were generally poorly or apparently not corrupted, indicating recent activity. Both Tor3 and Tor4b families bore an envelope-like open reading frame, suggesting possible horizontal acquisition through infection. The Tor4b envelope-like gene might have been obtained from a paramyxovirus (RNA virus). Tor3 and Tor4b are phylogenetically clearly distinct from vertebrate retroviruses (Retroviridae) and are more reminiscent of certain insect and plant sequences. Tor elements potentially represent a so far unknown, ancient type of infectious retroelement in chordates. Their distribution and transmission dynamics in tunicates and other chordates deserve further study.