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The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Open accessAbstract
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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Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp348 · Cited by 12,751
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,702
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H.-H., Rognes, T., & Ussery, D. W. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm160 · Cited by 6,112
HMMER web server: interactive sequence similarity searching
Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952
The Microbial Engines That Drive Earth's Biogeochemical Cycles
Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008) · Science · doi:10.1126/science.1153213 · Cited by 3,379
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Pruesse, E., Peplies, J., & Glöckner, F. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts252 · Cited by 3,079
Structure and function of the global ocean microbiome
Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., et al. (2015) · Science · doi:10.1126/science.1261359 · Cited by 2,921
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita, H., & Lam, T.-W. (2016) · Methods · doi:10.1016/j.ymeth.2016.02.020 · Cited by 2,079
A new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,887
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
(2017) · doi:10.1038/s41564-018-0171-1 · Cited by 1,742
De novo assembly of bacterial transcriptomes from RNA-seq data
Tjaden, B. (2015) · Genome Biology · doi:10.1186/s13059-014-0572-2 · Cited by 1,717
Staley, J. T., & Konopka, A. (1985) · Annual Review of Microbiology · doi:10.1146/annurev.mi.39.100185.001541 · Cited by 1,570
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013) · Nature Biotechnology · doi:10.1038/nbt.2579 · Cited by 1,251
Anantharaman, K., Brown, C. T., Hug, L. A., Sharon, I., Castelle, C. J., Probst, A. J., Thomas, B. C., Singh, A., Wilkins, M. J., Karaoz, U., et al. (2016) · Nature Communications · doi:10.1038/ncomms13219 · Cited by 1,136
Benson, D. A. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.15 · Cited by 833
The Pfam Protein Families Database
Bateman, A. G., Birney, E., Cerruti, L., Durbin, R. M., Etwiller, L., Eddy, S. R., Griffiths‐Jones, S., Howe, K., Marshall, M. S., & Sonnhammer, E. L. L. (2002) · PubMed Central · Cited by 764
Gene and translation initiation site prediction in metagenomic sequences
Hyatt, D., LoCascio, P. F., Hauser, L. J., & Uberbacher, E. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts429 · Cited by 651
Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T., Rappé, M. S., McLellan, S. L., Lücker, S., & Eren, A. M. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0176-9 · Cited by 602
A holistic approach to marine eco-systems biology
Karsenti, E., Acinas, S. G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.-M., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001177 · Cited by 477
Open science resources for the discovery and analysis of Tara Oceans data
Pesant, S., Not, F., Picheral, M., Kandels-Lewis, S., Le Bescot, N., Gorsky, G., Iudicone, D., Karsenti, E., Speich, S., Troublé, R., et al. (2015) · Scientific Data · doi:10.1038/sdata.2015.23 · Cited by 431
Potential for primary productivity in a globally-distributed bacterial phototroph
Graham, E. D., Heidelberg, J. F., & Tully, B. J. (2018) · The ISME Journal · doi:10.1038/s41396-018-0091-3 · Cited by 286
Self-citationMoran, M. A. (2015) · Science · doi:10.1126/science.aac8455 · Cited by 261
Metagenome-assembled genomes uncover a global brackish microbiome
Hugerth, L. W., Larsson, J., Alneberg, J., Lindh, M. V., Legrand, C., Pinhassi, J., & Andersson, A. F. (2015) · Genome Biology · doi:10.1186/s13059-015-0834-7 · Cited by 249
Santos, S. R., & Ochman, H. (2004) · Environmental Microbiology · doi:10.1111/j.1462-2920.2004.00617.x · Cited by 240
Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers
Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., & Lamborg, C. H. (2014) · Science · doi:10.1126/science.1256450 · Cited by 215
Next Generation Sequence Assembly with AMOS
Treangen, T. J., Sommer, D. D., Angly, F. E., Koren, S., & Pop, M. (2011) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1108s33 · Cited by 212
Expression patterns reveal niche diversification in a marine microbial assemblage
Gifford, S. M., Sharma, S., Booth, M., & Moran, M. A. (2013) · The ISME Journal · doi:10.1038/ismej.2012.96 · Cited by 200
Seitz, K. W., Lazar, C. S., Hinrichs, K.-U., Teske, A. P., & Baker, B. J. (2016) · The ISME Journal · doi:10.1038/ismej.2015.233 · Cited by 198
Farrant, G. K., Doré, H., Cornejo-Castillo, F. M., Partensky, F., Ratin, M., Ostrowski, M., Pitt, F. D., Wincker, P., Scanlan, D. J., Iudicone, D., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1524865113 · Cited by 195
Graham, E. D., Heidelberg, J. F., & Tully, B. J. (2017) · PeerJ · doi:10.7717/peerj.3035 · Cited by 187
Self-citation290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology
Tully, B., Sachdeva, R., Graham, E. D., & Heidelberg, J. F. (2017) · PeerJ · doi:10.7717/peerj.3558 · Cited by 103
Self-citationPotential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments
Tully, B., & Heidelberg, J. F. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.01023-16 · Cited by 44
Self-citation
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Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
Chen, I.-M. A., Chu, K., Palaniappan, K., Pillay, M., Ratner, A., Huang, J., Huntemann, M., Varghese, N., White, J. R., Seshadri, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky901 · Cited by 835
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737
Tara Oceans: towards global ocean ecosystems biology
Sunagawa, S., Acinas, S. G., Bork, P., Bowler, C., Coordinators, T. O., Acinas, S. G., Babin, M., Bork, P., Boss, E., Bowler, C., et al. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0364-5 · Cited by 490
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
Castelle, C. J., Brown, C. T., Anantharaman, K., Probst, A. J., Huang, R. H., & Banfield, J. F. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0076-2 · Cited by 454
Metadata
- Authors
- Tully, B. J., Graham, E. D., & Heidelberg, J. F.
- Venue
- Scientific Data
- Published
- 2018-01-16
- Volume
- 5
- Issue
- 1
- Pages
- 170203-170203
- ISSN
- 2052-4463 (ISSN-L)
- OpenAlex
- W2735611463
- Cited by
- 508
- References
- 42
- Type
- data paper
- Language
- en
- Open access
- gold
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