A catalogue of 136 microbial draft genomes from Red Sea metagenomes

Scientific Data

Volumn 3, Issue , 2016, Pages

  Haroon, Mohamed F ^a   Thompson, Luke R ^a,b   Parks, Donovan H ^c   Hugenholtz, Philip ^c   Stingl, Ulrich ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; SEA WATER;

BACTERIUM; DNA SEQUENCE; ECOSYSTEM; GENETICS; INDIAN OCEAN; METAGENOME; METAGENOMICS; MICROBIAL GENOME; MICROFLORA; MOLECULAR GENETICS; PHYLOGENY; SALINITY; TEMPERATURE;

BACTERIA; ECOSYSTEM; GENOME, MICROBIAL; INDIAN OCEAN; METAGENOME; METAGENOMICS; MICROBIOTA; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SALINITY; SEAWATER; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 84977544966     PISSN: None     EISSN: 20524463     Source Type: Journal    
DOI: 10.1038/sdata.2016.50     Document Type: Article

References (44)

1. Thompson, L. R. et al. Metagenomic covariation along densely sampled environmental gradients in the Red Sea. bioRxiv doi:10.1101/055012 (2016).
2. Churchill, J. H., Bower, A. S., McCorkle, D. C., Abualnaja, Y. The transport of nutrient-rich Indian Ocean water through the Red Sea and into coastal reef systems. Journal of Marine Research 72, 165-181 (2014).
3. Sagar, S. et al. Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea. BMC Complementary and Alternative Medicine 13, 1-8 (2013).
4. Jimenez-Infante, F. et al. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. FEMS microbiology ecology 89, 181-197 (2014).
5. Zhang, G., Haroon, M. F., Zhang, R., Hikmawan, T., Stingl, U. Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea. Genome Announcements 4, e00109-16 (2016).
6. Fuller, N. J. et al. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Applied and Environmental Microbiology 69, 2430-2443 (2003).
7. Qian, P.-Y. et al. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. The ISME journal 5, 507-518 (2011).
8. Ngugi, D. K., Stingl, U. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro-and macrodiversity of SAR11 populations in the Red Sea. PLoS ONE 7, e50274 (2012).
9. Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013).
10. Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208-211 (2015).
11. Grötzinger, S. W. et al. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). Frontiers in Microbiology 5, 134 (2014).
12. Clingenpeel, S., Clum, A., Schwientek, P., Rinke, C., Woyke, T. Reconstructing each cell's genome within complex microbial communities-dream or reality Frontiers in Microbiology 5 (2015).
13. Gawad, C., Koh, W., Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175-188 (2016).
14. Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology 31, 533-538 (2013).
15. Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotech. 32, 822-828 (2014).
16. Sangwan, N., Xia, F., Gilbert, J. A. Recovering complete and draft population genomes from metagenome datasets. Microbiome 4, 1-11 (2016).
17. Haroon, M. F. et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500, 567-570 (2013).
18. Soo, R. M. et al. An expanded genomic representation of the phylum Cyanobacteria. Genome biology and evolution 6, 1031-1045 (2014).
19. Evans, P. N. et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350, 434-438 (2015).
20. Moore, L. R., Rocap, G., Chisholm, S. W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393, 464-467 (1998).
21. Partensky, F., Hess, W., Vaulot, D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiology and molecular biology reviews 63, 106-127 (1999).
22. Moore, L. R., Goericke, R., Chisholm, S. W. Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties. Marine ecology progress series. Oldendorf 116, 259-275 (1995).
23. Palenik, B. et al. The genome of a motile marine Synechococcus. Nature 424, 1037-1042 (2003).
24. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63 (1990).
25. Britschgi, T. B., Giovannoni, S. J. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Applied and Environmental Microbiology 57, 1707-1713 (1991).
26. Haroon, M. F., Thompson, L. R., Stingl, U. Draft genome sequence of uncultured SAR324 bacterium lautmerah10, binned from a Red Sea metagenome. Genome Announcements 4, e01711-e01715 (2016).
27. Ivars-Martinez, E. et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. The ISME journal 2, 1194-1212 (2008).
28. Santoro, A. E. et al. Genomic and proteomic characterization of 'Candidatus Nitrosopelagicus brevis': An ammonia-oxidizing archaeon from the open ocean. Proceedings of the National Academy of Sciences 112, 1173-1178 (2015).
29. DeLong, E. F. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences 89, 5685-5689 (1992).
30. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
31. Bull, A. T., Stach, J. E. Marine actinobacteria: new opportunities for natural product search and discovery. Trends in microbiology 15, 491-499 (2007).
32. Markowitz, V. M. et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Research 40, D115-D122 (2012).
33. Rusch, D. et al. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biology 5, e77 (2007).
34. Schmieder, R., Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864 (2011).
35. Peng, Y., Leung, H. C., Yiu, S.-M., Chin, F. Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
36. Li, H., Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
37. Kang, D. D., Froula, J., Egan, R., Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).
38. Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25, 1043-1055 (2015).
39. Eddy, S. R. Accelerated Profile HMM Searches. PLoS Computational Biology 7, e1002195 (2011).
40. Price, M. N., Dehal, P. S., Arkin, A. P. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
41. Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 (1985).
42. Dagan, T., Roettger, M., Bryant, D., Martin, W. Genome Networks Root the Tree of Life between Prokaryotic Domains. Genome Biology and Evolution 2, 379-392 (2010).
43. Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Research 32, 1363-1371 (2004).
44. Letunic, I., Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 39, W475-W478 (2011).