1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

By Supratim Mukherjee, Rekha Seshadri, Neha J. Varghese, Emiley A. Eloe-Fadrosh, Jan P. Meier-Kolthoff, Markus Göker, R. Coates, Michalis Hadjithomas, Georgios A Pavlopoulos, David Páez-Espino and 11 more. 2017

243 citations recorded by the source corpus.

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.

Subfields: Food Science, Molecular Biology, Pharmacology

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Citations in the corpus

Evolution of resilience in protein interactomes across the tree of life (2018, background): “DNA sequence information has been used to associate genes with their functions (11), determine properties of ancestral life (12, 13), and understand how the environment affects genomes (14).”
Genome-Based Taxonomic Classification of the Phylum Actinobacteria (2018, methodology): “, 2009), that originated from the Genomic Encyclopedia of Archaea and Bacteria pilot phase or phase 1 of the One Thousand Microbial Genomes project (Kyrpides et al., 2014; Mukherjee et al., 2017).”
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI (2018, unknown): “Cooperative projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which is focused on expanding phylogenetic diversity of prokaryotic genomes and types [6, 7], are rapidly expanding taxonomic coverage for type strain genomes.”