The evolution of tyrosine-recombinase elements in Nematoda.
The evolution of tyrosine-recombinase elements in Nematoda.
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DOI：
10.1371/journal.pone.0106630
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Lunt DH
中科院分区：
文献类型：
--
作者：
Szitenberg A;Koutsovoulos G;Blaxter ML;Lunt DH
转座因子根据其转座机制可分为DNA和RNA两大类。酪氨酸重组酶元件（YRE）是相对罕见的和知之甚少，尽管共享的DNA和RNA元件的特性。以前，已报道的线虫类有一个实质上不同的多样性的YRE相比，其他动物门：Dirs1样YRE反转录转座子中遇到的大多数动物门，但不是在线虫，和一个独特的Pat1样YRE反转录转座子只记录了线虫。我们探讨了YRE的多样性，线虫类广泛的门，包括34个基因组代表线虫类内的三个类采样。我们开发了一种方法来隔离和分类YRE的基础上的功能组织和系统发育关系，在一个开放的和可重复的工作流程。我们还确保我们的系统发育方法YRE分类确定截断和退化的元素，信息增加采样的元素数量。我们确定了Dirs1样元素（认为是缺席线虫类）在线虫纲Enoplia和Dorylaimia表明线虫模式物种不足以代表门中的转座因子的多样性。线虫Pat1样元件被发现是另一种Pat1样元件的衍生形式，该元件在动物中更广泛地存在。发现广泛用于YRE分类的几个序列特征是同源的，突出了对基于遗传学的分类方案的需要。线虫模式种不能代表该门转座因子的多样性。
Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.
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影响因子：
6.5
作者：
Anisimova M;Gil M;Dufayard JF;Dessimoz C;Gascuel O
通讯作者：
Gascuel O
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
10.7
作者：
Goodwin, TJD;Poulter, RTM
通讯作者：
Poulter, RTM
DOI：
10.1073/pnas.1119667109
发表时间：
2012-01-17
影响因子：
11.1
作者：
Eads, Brian D.;Tsuchiya, Dai;Zolan, Miriam E.
通讯作者：
Zolan, Miriam E.
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T