Loiseau Vincent, Herniou Elisabeth A, Moreau Yannis, Lévêque Nicolas, Meignin Carine, Daeffler Laurent, Federici Brian, Cordaux Richard, Gilbert Clément
Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique et Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Saclay, Gif-sur-Yvette 91198, France.
Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, 37200 Tours, France.
Virus Evol. 2020 Jan 27;6(1):vez060. doi: 10.1093/ve/vez060. eCollection 2020 Jan.
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double-stranded (ds) DNA viruses is limited. Here, we sequenced the genome of a baculovirus ( multiple nucleopolyhedrovirus [AcMNPV]) purified from beet armyworm () larvae at depths >195,000× using both short- (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications, and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9 per cent of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after ten replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1,102 SVs carried by 52.4-80.1 per cent of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
我们对双链（ds）DNA大病毒群体中基因组结构变异的多样性和频率的了解有限。在这里，我们使用短读长（Illumina）和长读长（PacBio）技术，对从甜菜夜蛾幼虫中纯化的杆状病毒（多粒核型多角体病毒[AcMNPV]）基因组进行了深度大于195,000倍的测序。使用一个依赖于六个变异检测工具在单个短读长和长读长中检测到的结构变异（SVs）层次聚类的流程，我们在AcMNPV中总共鉴定出1141个SVs，包括464个缺失、443个倒位、160个重复和74个插入。这些变异被认为是可靠的，不太可能是技术假象导致的，因为它们在至少三个长读长以及至少三个短读长中被独立检测到。SVs分布在整个AcMNPV基因组中，可能涉及大的基因组区域（平均30,496 bp）。我们发现，在AcMNPV群体中，不少于39.9%的基因组携带至少一个SV，绝大多数SV（75%）以非常低的频率（<0.01%）分离，并且在十个复制周期后只有极少数SV持续存在，这与大多数SV对AcMNPV适应性的负面影响一致。然后，使用短读长测序数据集，我们表明两种虹彩病毒和一种疱疹病毒的群体中也充满了SVs，因为它们的基因组中有52.4 - 80.1%携带426到1102个SVs。最后，AcMNPV的长读长使我们能够鉴定出1757个转座元件（TEs）插入，其中895个是截短的，并且发生在读长的一端。这进一步支持了杆状病毒作为TEs水平转移可能载体的作用。总之，我们发现SVs在病毒群体中主要在快速的得失动态下进化，是大型dsDNA病毒生物学的一个重要特征。
