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. 2018 Jan 16:5:170203.
doi: 10.1038/sdata.2017.203.

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Benjamin J Tully  1 , Elaina D Graham  2 , John F Heidelberg  1   2
Affiliations

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Benjamin J Tully et al. Sci Data. .

Abstract

Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ≥2 kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. A map depicting the approximate locations of the Tara Oceans sampling stations from which metagenomics data was collected.
Stations are grouped in to larger provinces based on Longhurst Provinces and site proximity. Province abbreviations are used for draft genome IDs. The map in Fig. 1 were modified under a CC BY-SA 3.0 license from ‘Oceans and Seas boundaries map’ by Pinpin.
Figure 2
Figure 2. A maximum likelihood tree of the TOBG draft genomes based on 16 concatenated single-copy phylogenetic markers.
Bootstrap values >0.75 are shown. Circle size representing the bootstrap value is scaled from 0.75–1.0. Nodes where the average branch length distance is <0.5 were collapsed and the number of draft genomes in each node are provided. The image was generated using the Interactive Tree of Life (iTOL; http://itol.embl.de/).
Figure 3
Figure 3
See this image and copyright information in PMC

Dataset use reported in

References

Data Citations

    1. Tully B. J. 2017. NCBI BioProject. PRJNA391943
    1. Tully B. J. 2017. Figshare. http://dx.doi.org/10.6084/m9.figshare.5188273 - DOI

References

    1. Moran M. A. The global ocean microbiome. Science 350, aac8455 (2015). - PubMed
    1. Falkowski P. G., Fenchel T. & DeLong E. F. The Microbial Engines That Drive Earth's Biogeochemical Cycles. Science 320, 1034–1039 (2008). - PubMed
    1. Staley J. T. & Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annual Reviews in Microbiology 39, 321–346 (1985). - PubMed
    1. Tyson G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004). - PubMed
    1. Seitz K. W., Lazar C. S., Hinrichs K.-U., Teske A. P. & Baker B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J 10, 1696–1705 (2016). - PMC - PubMed

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