A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

By Dongying Wu, Philip Hugenholtz, K. Mavromatis, R. Pukall, Eileen Dalin, Natalia N. Ivanova, Victor Kunin, Lynne A. Goodwin, Martin Wu, Brian J. Tindall and 24 more. Nature, 2009

1,012 citations recorded by the source corpus.

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/64325c7c915312fcd362217761f8eab132cc2a0f

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Citations in the corpus

Animals in a bacterial world, a new imperative for the life sciences (2013, background): “This game-changing advance catalyzed a rapid development and application of molecular sequencing technologies, which allowed biologists for the first time to recognize the true diversity, ubiquity, and functional capacity of microorganisms (2).”
Rfam: Wikipedia, clans and the “decimal” release (2010, background): “Sequencing projects such as the Genome 10K (48) and other attempts to fill sequencing gaps in the tree of life (49) mean that most Rfam families will dramatically increase in depth in the near future.”
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata (2011, neutral): “(5) has actually increased during the last couple of years from 80% to 86% today despite the large-scale sequencing efforts, such as the GEBA (7) and HMP (6), which target previously neglected phylogenetic lineages (Figure 1D).”
Microbial species delineation using whole genome sequences (2015, background): “…the domain wide application of ANI, which was infeasible a few years ago, has become practical, effective and scalable with the novel variation of AF and gANI computation, as well as value-enriched and made necessary by the recent increase of phylogenetic coverage with whole genome sequences (7,8).”
IMG/M 4 version of the integrated metagenome comparative analysis system (2013, background): “Genomes generated as part of the Microbial Dark Matter project (18), which aims to use single cell genomics to expand the Genomic Encyclopedia of Bacteria and Archaea (19) by targeting single cell representatives of uncultured candidate phyla are of particular importance to the breadth of the refere”
VIROME: a standard operating procedure for analysis of viral metagenome sequences (2012, background): “The disconnect be-tween taxonomy and function has been a driving rationale behind microbial Genomic Encyclopedia of Bacteria and Archaea efforts such as the [10,11].”
PhyloSift: phylogenetic analysis of genomes and metagenomes (2014, background): “Efforts to increase the phylogenetic diversity of available genome sequences are ongoing (Wu et al., 2009; Rinke et al., 2013; Shih et al., 2013) Advances in the preparation of high throughput samples will make comparative metagenomics more tractable.”
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (2011, background): “The majority of bacterial phyla are known only from 16S surveys and have no cultured representatives (Rappe and Giovannoni 2003 ; Wu et al. 2009).”
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance (2012, methodology): “The method we present in this study can be used with any set of reference sequences, and as greater numbers of genomes from uncultured and phylogenetically diverse microbes are sequenced [28], we expect that our ability to estimate copy number and abundance will become even more accurate.”
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014, background): “Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2].”