Dataset Information

Clades of huge phages from across Earth's ecosystems.

ABSTRACT: Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

SUBMITTER: Al-Shayeb B

PROVIDER: S-EPMC7162821 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Clades of huge phages from across Earth's ecosystems.

Al-Shayeb Basem B Sachdeva Rohan R Chen Lin-Xing LX Ward Fred F Munk Patrick P Devoto Audra A Castelle Cindy J CJ Olm Matthew R MR Bouma-Gregson Keith K Amano Yuki Y He Christine C Méheust Raphaël R Brooks Brandon B Thomas Alex A Lavy Adi A Matheus-Carnevali Paula P Sun Christine C Goltsman Daniela S A DSA Borton Mikayla A MA Sharrar Allison A Jaffe Alexander L AL Nelson Tara C TC Kantor Rose R Keren Ray R Lane Katherine R KR Farag Ibrahim F IF Lei Shufei S Finstad Kari K Amundson Ronald R Anantharaman Karthik K Zhou Jinglie J Probst Alexander J AJ Power Mary E ME Tringe Susannah G SG Li Wen-Jun WJ Wrighton Kelly K Harrison Sue S Morowitz Michael M Relman David A DA Doudna Jennifer A JA Lehours Anne-Catherine AC Warren Lesley L Cate Jamie H D JHD Santini Joanne M JM Banfield Jillian F JF

Nature 20200212 7795

Bacteriophages typically have small genomes<sup>1</sup> and depend on their bacterial hosts for replication<sup>2</sup>. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undes ...[more]

PMID: 32051592

Similar Datasets

Project description:Abstract Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991–3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses—amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.

Dataset Information

Clades of huge phages from across Earth's ecosystems.

Publications

Clades of huge phages from across Earth's ecosystems.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets