Jacopo Martelossi, Mariangela Iannello, Fabrizio Ghiselli, Andrea Luchetti
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In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution.</p><p><strong>Results: </strong>We found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a \"mosaic\" evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions.</p><p><strong>Conclusion: </strong>Here we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. 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They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution.</p><p><strong>Results: </strong>We found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a \\\"mosaic\\\" evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. 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引用次数: 0
摘要
背景:短间隔核元素(SINEs)是广泛存在于真核生物中的非自主性非LTR逆转录转座子。它们既可以作为种系特异的快速进化元件而存在,也可以作为以高度保守结构域(HCD)为特征的无处不在的超家族而存在。这些超家族中有几个已经在双壳类动物中得到了描述,但由于双壳类动物的转座子文库极其稀少,它们的总体分布及其对宿主基因组进化的影响仍然未知。在这项研究中,我们研究了 40 多个双壳类基因组,以揭示 HCD-tRNA 相关 SINE 的分布,发现新的 SINE-LINE 伙伴关系,并了解它们在塑造双壳类基因组进化过程中可能扮演的角色:结果:我们发现双壳类动物的HCD SINEs起源古老,它们至少依赖于四个不同的LINE支系。根据 "马赛克 "进化设想,多个 LINE 伙伴可促进相同 HCD SINE 超家族的扩增,而同源 LINE 衍生的尾部则存在于不同超家族之间。研究发现,多个 SINEs 在系统发育相关的物种之间高度相似,但它们之间的进化时间尺度却极长,最长可达 4 亿年。通过研究它们在五个物种亚群中的基因组分布,我们观察到 SINE 在不同基因组区块中的富集模式不同,而且 SINE 在内含子序列中形成串联结构和回文结构的趋势也不同。尽管存在这些差异,但我们观察到,SINEs,尤其是较老的 SINEs,倾向于优先在基因内或基因附近积累,这与有害性较低的短非编码转座子在染色体外基因组区域的生存偏倚模型是一致的:在这里,我们对双壳类动物中与 tRNA 相关的 SINEs 进行了广泛的特征描述,揭示了它们在分类学上的分布以及整个类群中的 LINE 伙伴关系。此外,通过研究它们在五个物种中的基因组分布,我们强调了它们与之前研究过的其他真核生物的共同点和不同点,从而扩展了我们对整个生命树中 SINE 演化的了解。
Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions.
Background: Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution.
Results: We found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a "mosaic" evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions.
Conclusion: Here we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. Moreover, through the study of their genomic distribution in five species, we highlighted commonalities and differences with other previously studied eukaryotes, thus extending our understanding of SINE evolution across the tree of life.
期刊介绍:
Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.