Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains.

William B Whitman,Yuguang Zhou,George Garrity,Paul De Vos,Tanja Woyke,Philip Hugenholtz,Timothy G Lilburn,Hans-Peter Klenk,Jonathan A Eisen,Nikos C Kyrpides,Brian J Beck,Peter Vandamme

doi:10.1186/s40793-015-0017-x

Abstract

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.

Highlights

The Genomic Encyclopedia of Bacteria and Archaea was launched in 2007 with the aim of sequencing 250 type strains from branches of the tree of life with low sequence representation [1]
The Genomic Encyclopedia of Bacteria and Archaea (GEBA) pilot project, which encompassed the first 56 genomes, provided convincing evidence of the value of a phylogeny-driven selection of target strains for the discovery of new protein families and enhancing the accuracy of sequence binning methods commonly used in metagenome projects [1,2,3,4]
In 2012, GEBA was extended with the project entitled Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project [5]

Summary

Introduction

The Genomic Encyclopedia of Bacteria and Archaea was launched in 2007 with the aim of sequencing 250 type strains from branches of the tree of life with low sequence representation [1]. Phase II: from individual species to whole genera, targeted another 1000 genome sequences and strain selection shifted to complete clusters of all the type strains in selected genera and small families This approach was enabled by the pipeline developed in KMG-I to automate most steps from sequencing, to annotation, and data deposition. We note that there has been an associated “microbial dark matter” project at DOE-JGI to sequence the genomes of phylogenetically novel, uncultured taxa using a single cell whole genome amplification strategy (see[6]) First results from that project have been published [7], and it too has moved into its own advanced phase. This project is not discussed further since our focus is on cultured organisms

Objectives

Findings

Conclusion