Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats.
Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats.
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DOI：
10.1186/s12915-015-0202-9
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发表时间：
2015-11-04
期刊：
影响因子：
5.4
通讯作者：
Barraclough TG
中科院分区：
文献类型：
--
作者：
Eyres I;Boschetti C;Crisp A;Smith TP;Fontaneto D;Tunnacliffe A;Barraclough TG
虽然在原核生物中普遍存在，但水平基因转移（HGT）在多细胞真核生物中较为罕见。蛭形轮虫是显微镜下的动物，其基因组中含有比典型动物更高比例的水平转移的非后生动物基因。据推测，蛭形目昆虫在修复因干燥引起的双链断裂后的染色体时会掺入外源DNA。因此，HGT可能有助于物种的分化和适应，就像在原核生物中一样。如果是这样的话，我们认为物种应该在外来基因的互补方面有所不同，而不是共享从共同祖先继承的同一套外来基因。此外，在干燥更频繁的物种中应该有更多的外源基因。我们测试了这些假设，通过调查HGT在四个同属种蛭形类来自不同的栖息地：两个永久性水生栖息地和两个临时水生栖息地，定期干燥。所有四个物种的转录组包含许多基因与非后生动物基因比后生动物基因更接近匹配。一个物种的全基因组测序证实了这些外源基因在基因组中的存在。近一半的外源基因在所有四个物种和来自另一个家族的外群之间共享，但数百个是特定物种所独有的，这表明HGT正在进行中。使用一个过时的基因组，我们估计每百万年平均有12.8个外来基因的增加和2.0个外来基因的丢失。与干燥假说相一致，HGT的水平在经历定期干燥事件的物种中高于那些不经历干燥事件的物种。然而，HGT仍然贡献了数百个外来基因的物种从永久水生栖息地。外源基因主要是具有多种功能的酶，包括复合多糖的催化和胁迫反应。我们发现的证据差异损失的祖先外来基因以前与干燥保护在两个非干燥的物种。近一半的外源基因是在蛭形虫科分化之前获得的。尽管如此，HGT正在蛭类动物中进行，并有助于物种之间的假定功能差异。我们的研究物种之间的变化是一致的假设，干燥的栖息地促进HGT。本文的在线版本（doi：10.1186/s12915-015-0202-9）包含补充材料，可供授权用户使用。
Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly. Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species. Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT. The online version of this article (doi:10.1186/s12915-015-0202-9) contains supplementary material, which is available to authorized users.