IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
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DOI：
10.1093/nar/gkac1037
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发表时间：
2022-11-18
影响因子：
14.9
通讯作者：
Roux, Simon
中科院分区：
文献类型：
--
作者：
Camargo, Antonio Pedro;Nayfach, Stephen;Roux, Simon
病毒被广泛认为是所有微生物组的关键成员。宏基因组学使全球病毒圈的大规模探索成为可能，逐步揭示了地球上广泛的病毒基因组多样性，并突出了病毒影响生物过程的无数方式。IMG/VR提供了对从（Meta）基因组获得的最大病毒序列集合的访问，沿着功能注释和丰富的元数据。网络界面使用户能够有效地浏览和搜索基于基因组特征和/或序列相似性的病毒。在这里，我们介绍了IMG/VR的第四个版本，由超过1500万个病毒基因组和基因组片段组成，与前一个版本相比，其大小增加了6倍。这些分类单位可分为870万个病毒操作分类单位，其中231408个单位至少有一个高质量的代表。IMG/VR中的病毒序列现在使用一种新的检测方法（geNomad）从基因组、宏基因组和元转录组中系统地鉴定，IMG标准注释与使用Rankov的基因组质量估计、反映最新分类标准的分类分类和微生物宿主分类预测相补充。IMG/VR v4可通过https：//img.jgi.doe.gov/vr获得，基础数据可通过https：//www.example.com下载。genome.jgi.doe.gov/portal/IMGVR
Viruses are widely recognized as critical members ofall microbiomes. Metagenomics enables large-scaleexploration of the global virosphere, progressivelyrevealing the extensive genomic diversity of viruseson Earth and highlighting the myriad of ways bywhich viruses impact biological processes. IMG/VRprovides access to the largest collection of viral se-quences obtained from (meta)genomes, along withfunctional annotation and rich metadata. A web inter-face enables users to efficiently browse and searchviruses based on genome features and/or sequencesimilarity. Here, we present the fourth version ofIMG/VR, composed of > 15 million virus genomesand genome fragments, a asymptotic to 6-fold increase in sizecompared to the previous version. These clusteredinto 8.7 million viral operational taxonomic units, in-cluding 231 408 with at least one high-quality repre-sentative. Viral sequences in IMG/VR are now sys-tematically identified from genomes, metagenomes,and metatranscriptomes using a new detection ap-proach (geNomad), and IMG standard annotation arecomplemented with genome quality estimation us-ing CheckV, taxonomic classification reflecting thelatest taxonomic standards, and microbial host tax-onomy prediction. IMG/VR v4 is available athttps://img.jgi.doe.gov/vr, and the underlying data areavailable to download athttps://genome.jgi.doe.gov/portal/IMGVR.