IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

被引：224

作者：

Roux, Simon ^{[1
]}

Paez-Espino, David ^{[1
]}

Chen, I-Min A. ^{[1
]}

Palaniappan, Krishna ^{[1
]}

Ratner, Anna ^{[1
]}

Chu, Ken ^{[1
]}

Reddy, T. B. K. ^{[1
]}

Nayfach, Stephen ^{[1
]}

Schulz, Frederik ^{[1
]}

Call, Lee ^{[1
]}

Neches, Russell Y. ^{[1
]}

Woyke, Tanja ^{[1
]}

Ivanova, Natalia N. ^{[1
]}

Eloe-Fadrosh, Emiley A. ^{[1
]}

Kyrpides, Nikos C. ^{[1
]}

机构：

[1] Lawrence Berkeley Natl Lab, DOE Joint Genome Inst, Berkeley, CA 94720 USA

来源：

NUCLEIC ACIDS RESEARCH | 2021年 / 49卷 / D1期

关键词：

VIRAL ECOLOGY; DNA; BACTERIAL; TAXONOMY; WORLD; PHAGE;

D O I：

10.1093/nar/gkaa946

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbialcommunity structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The newIMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity.

引用

页码：D764 / D775

页数：12

共 62 条

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