Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France.
Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, 29688, Roscoff, France.
BMC Genomics. 2018 Nov 15;19(1):821. doi: 10.1186/s12864-018-5200-1.
The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested that Copia LTR-retrotransposons display specific dynamic compared to the more abundant and diverse Gypsy elements. Indeed, Copia elements show a relative scarcity and the prevalence of only a few clades in specific hosts. Thus, BEL/Pao seems to be the second most abundant superfamily. However, the generality of these assumptions remains to be assessed. Therefore, we carried out the first large-scale comparative genomic analysis of LTR-retrotransposons in molluscs. The aim of this study was to analyse the diversity, copy numbers, genomic proportions and distribution of LTR-retrotransposons in a large host phylum.
We compare nine genomes of molluscs and further added LTR-retrotransposons sequences detected in databases for 47 additional species. We identified 1709 families, which enabled us to define 31 clades. We show that clade richness was highly dependent on the considered superfamily. We found only three Copia clades, including GalEa and Hydra which appear to be widely distributed and highly dominant as they account for 96% of the characterised Copia elements. Among the seven BEL/Pao clades identified, Sparrow and Surcouf are characterised for the first time. We find no BEL or Pao elements, but the rare clades Dan and Flow are present in molluscs. Finally, we characterised 21 Gypsy clades, only five of which had been previously described, the C-clade being the most abundant one. Even if they are found in the same number of host species, Copia elements are clearly less abundant than BEL/Pao elements in copy number or genomic proportions, while Gypsy elements are always the most abundant ones whatever the parameter considered.
Our analysis confirms the contrasting dynamics of Copia and Gypsy elements in metazoans and indicates that BEL/Pao represents the second most abundant superfamily, probably reflecting an intermediate dynamic. Altogether, the data obtained in several taxa highly suggest that these patterns can be generalised for most metazoans. Finally, we highlight the importance of using database information in complement of genome analyses when analyzing transposable element diversity.
长末端重复（LTR）反转录转座子的三个超家族是一种广泛存在的转座元件，也是真核生物基因组进化的主要因素。在后生动物中，最近的研究表明，与更为丰富和多样的 Gypsy 元件相比，Copia LTR 反转录转座子表现出特定的动态。事实上，Copia 元件的相对丰度较低，仅在特定宿主中流行少数几个分支。因此，BEL/Pao 似乎是第二丰富的超家族。然而，这些假设的普遍性仍有待评估。因此，我们对软体动物进行了 LTR 反转录转座子的首次大规模比较基因组分析。本研究的目的是分析在一个大的宿主门中 LTR 反转录转座子的多样性、拷贝数、基因组比例和分布。
我们比较了 9 种软体动物的基因组，并进一步添加了数据库中 47 个额外物种的 LTR 反转录转座子序列。我们鉴定了 1709 个家族，从而能够定义 31 个分支。我们表明，分支丰富度高度依赖于所考虑的超家族。我们只发现了三个 Copia 分支，其中包括 GalEa 和 Hydra，它们似乎分布广泛且高度占主导地位，因为它们占已鉴定的 Copia 元件的 96%。在鉴定的七个 BEL/Pao 分支中，Sparrow 和 Surcouf 是首次被描述的。我们没有发现 BEL 或 Pao 元件，但在软体动物中存在罕见的分支 Dan 和 Flow。最后，我们鉴定了 21 个 Gypsy 分支，其中只有 5 个之前有过描述，C 分支是最丰富的。即使在相同数量的宿主物种中发现，Copia 元件在拷贝数或基因组比例上的丰度明显低于 BEL/Pao 元件，而 Gypsy 元件无论考虑哪个参数都是最丰富的。
我们的分析证实了后生动物中 Copia 和 Gypsy 元件的动态对比，并表明 BEL/Pao 代表第二丰富的超家族，可能反映了一种中等动态。总的来说，从几个类群获得的数据强烈表明，这些模式可以推广到大多数后生动物。最后，我们强调了在分析转座元件多样性时，使用数据库信息补充基因组分析的重要性。
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