Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix-Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France.
Mol Biol Evol. 2023 Nov 3;40(11). doi: 10.1093/molbev/msad244.
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
类病毒科是感染变形虫的巨型病毒，拥有迄今已知的最大病毒粒子。自从从 3 万年前的永久冻土层样本中回收的西伯利亚类病毒（Pithovirus sibericum）被发现以来，其他类病毒和相关的 Cedratviruses 已从各种陆地和水生样本中分离出来。在这里，我们报告了从土壤样本中分离和基因组测序的 2 种类病毒科病毒，以及其他 3 种最近的分离物。利用 12 个可用的基因组序列，我们对类病毒科家族进行了全面的比较基因组研究，以破译它们基因组的组织和进化。我们的研究揭示了 2 个主要区域的非均匀基因组组织：1 个集中核心基因，另 1 个基因重复。我们还发现，类病毒科的基因组比其他巨型病毒家族更保守，来自水平转移的基因比例较低且稳定（5%至 7%）。家族内的基因组大小变化主要是由于基因重复率（14%至 28%）的变化和反向重复的大量入侵。虽然 Cedratviruses 中不存在这些重复元件，但重复丰富的区域覆盖了类病毒基因组的四分之一。使用专门的管道识别这些区域，是突变、基因捕获事件和基因组重排的热点，这些热点有助于它们的进化。
