PT  - JOURNAL ARTICLE
AU  - Al-Shayeb, Basem
AU  - Sachdeva, Rohan
AU  - Chen, Lin-Xing
AU  - Ward, Fred
AU  - Munk, Patrick
AU  - Devoto, Audra
AU  - Castelle, Cindy J.
AU  - Olm, Matthew R.
AU  - Bouma-Gregson, Keith
AU  - Amano, Yuki
AU  - He, Christine
AU  - Méheust, Raphaël
AU  - Brooks, Brandon
AU  - Thomas, Alex
AU  - Lavy, Adi
AU  - Matheus-Carnevali, Paula
AU  - Sun, Christine
AU  - Goltsman, Daniela S. A.
AU  - Borton, Mikayla A.
AU  - Nelson, Tara C.
AU  - Kantor, Rose
AU  - Jaffe, Alexander L.
AU  - Keren, Ray
AU  - Farag, Ibrahim F.
AU  - Lei, Shufei
AU  - Finstad, Kari
AU  - Amundson, Ronald
AU  - Anantharaman, Karthik
AU  - Zhou, Jinglie
AU  - Probst, Alexander J.
AU  - Power, Mary E.
AU  - Tringe, Susannah G.
AU  - Li, Wen-Jun
AU  - Wrighton, Kelly
AU  - Harrison, Sue
AU  - Morowitz, Michael
AU  - Relman, David A.
AU  - Doudna, Jennifer A
AU  - Lehours, Anne-Catherine
AU  - Warren, Lesley
AU  - Cate, Jamie H. D.
AU  - Santini, Joanne M.
AU  - Banfield, Jillian F.
TI  - Clades of huge phage from across Earth’s ecosystems
AID  - 10.1101/572362
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 572362
4099  - http://biorxiv.org/content/early/2019/03/11/572362.short
4100  - http://biorxiv.org/content/early/2019/03/11/572362.full
AB  - Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty-four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPR-Cas systems 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 phage may repurpose bacterial CRISPR-Cas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earth’s ecosystems.