Open Access1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Author(s) -
Supratim Mukherjee,
Rekha Seshadri,
Neha Varghese,
Emiley A. EloeFadrosh,
Jan P. MeierKolthoff,
Markus Göker,
Roger Coates,
Michalis Hadjithomas,
Georgios A. Pavlopoulos,
David Páez-Espino,
Yasuo Yoshikuni,
Axel Visel,
William B. Whitman,
George M Garrity,
Jonathan A. Eisen,
Philip Hugenholtz,
Amrita Pati,
Natalia Ivanova,
Tanja Woyke,
Hans Peter Klenk,
Nikos C. Kyrpides
Publication year - 2017
Publication title -
nature biotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 15.358
H-Index - 445
eISSN - 1546-1696
pISSN - 1087-0156
DOI - 10.1038/nbt.3886
Subject(s) - phylogenetic tree , genome , biology , archaea , computational biology , metagenomics , tree of life (biology) , phylogenetic diversity , bacterial genome size , phylogenetics , whole genome sequencing , genetics , function (biology) , evolutionary biology , gene
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.