Evolution and subfamilies of HERVL human endogenous retrovirus.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Bioinformatics advances Pub Date : 2024-07-30 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae110

Huan Zhang, Martin C Frith

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Abstract

Background: Endogenous retroviruses (ERVs), which blur the boundary between virus and transposable element, are genetic material derived from retroviruses and have important implications for evolution. This study examines the diversity and evolution of human endogenous retroviruses (HERVs) of the HERVL family, which has long terminal repeats (LTRs) named MLT2.

Results: By probability-based sequence comparison, we uncover systematic annotation errors that conceal the true complexity and diversity of transposable elements (TEs) in the human genome. Our analysis identifies new subfamilies within the MLT2 group, proposes a refined classification scheme, and constructs new consensus sequences. We present an evolutionary analysis including phylogenetic trees that elucidate the relationships between these subfamilies and their contributions to human evolution. The results underscore the significance of accurate TE annotation in understanding genome evolution, highlighting the potential for misclassified TEs to impact interpretations of genomic studies.

Availability and implementation: Not applicable.

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HERVL 人类内源性逆转录病毒的进化和亚家族。

背景：内源性逆转录病毒（ERVs）模糊了病毒和转座元件之间的界限，是逆转录病毒衍生的遗传物质，对进化具有重要意义。本研究考察了HERVL家族人类内源性逆转录病毒（HERVs）的多样性和进化，该家族的长末端重复序列（LTR）被命名为MLT2：通过基于概率的序列比较，我们发现了系统性的注释错误，这些错误掩盖了人类基因组中转座元件（TEs）的真实复杂性和多样性。我们的分析在 MLT2 群体中发现了新的亚家族，提出了一个完善的分类方案，并构建了新的共识序列。我们提出的进化分析包括系统发生树，阐明了这些亚家族之间的关系及其对人类进化的贡献。这些结果强调了准确的 TE 注释对理解基因组进化的重要意义，并突出了错误分类的 TE 可能会影响基因组研究的解释：不适用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

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0.00%

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