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dc.contributor.authorThompson, Luke R.
dc.contributor.authorHaroon, Mohamed F.
dc.contributor.authorShibl, Ahmed A.
dc.contributor.authorCahill, Matt J.
dc.contributor.authorNgugi, David K.
dc.contributor.authorWilliams, Gareth J.
dc.contributor.authorMorton, James T.
dc.contributor.authorKnight, Rob
dc.contributor.authorGoodwin, Kelly D.
dc.contributor.authorStingl, Ulrich
dc.date.accessioned2019-05-21T13:11:14Z
dc.date.available2019-05-21T13:11:14Z
dc.date.issued2019-02-15
dc.identifier.citationThompson, L. R., Haroon, M. F., Shibl, A. A., Cahill, M. J., Ngugi, D. K., Williams, G. J., … Stingl, U. (2019). Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes. Applied and Environmental Microbiology, 85(13). doi:10.1128/aem.00369-19
dc.identifier.issn0099-2240
dc.identifier.issn1098-5336
dc.identifier.doi10.1128/aem.00369-19
dc.identifier.doi10.1101/549816
dc.identifier.urihttp://hdl.handle.net/10754/653034
dc.description.abstractEvidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations upon conducive growth conditions. However, studies supporting this “microbial seed bank” hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the ocean; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, II) and 5Prochlorococcus(ecotype HLII) cells from the Red Sea and combined them with globally-sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically crypticProchlorococcusecotypes LLII and LLIII. Compared with reference genomes, 1% ofProchlorococcusand 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they could be functional. SearchingTaraOceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence-absence of OGs.
dc.description.sponsorshipWe thank Haiwei Luo for assistance building genome trees, Mamoon Rashid for consultation about decontamination methods, Qiyun Zhu for assistance with genome analysis, and Ramunas Stepanauskas and Nicole Poulton for assistance with the single-cell genomics protocol.
dc.publisherAmerican Society for Microbiology
dc.relation.urlhttps://aem.asm.org/content/early/2019/04/22/AEM.00369-19
dc.relation.urlhttp://biorxiv.org/lookup/doi/10.1101/549816
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
dc.subjectmetagenomics
dc.subjectPelagibacter
dc.subjectpopulation genomics
dc.subjectSAG
dc.subjectsingle-cell genomics
dc.titleRed Sea SAR11 andProchlorococcusSingle-cell Genomes Reflect Globally Distributed Pangenomes
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentMarine Science Program
dc.contributor.departmentOffice of the VP
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.identifier.journalApplied and Environmental Microbiology
dc.eprint.versionPre-print
dc.contributor.institutionOcean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, United States of America
dc.contributor.institutionDepartment of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, United States of America
dc.contributor.institutionSchool of Ocean Sciences, Bangor University, Anglesey, United Kingdom
dc.contributor.institutionDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, United States of America
dc.contributor.institutionDepartment of Pediatrics, University of California San Diego, La Jolla, CA, United States of America
dc.contributor.institutionCenter for Microbiome Innovation, University of California, San Diego, CA, United States of America
dc.contributor.institutionDepartment of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, UF/Institute of Food and Agricultural Sciences, University of FL, Davie, Florida, United States of America
kaust.personThompson, Luke R.
kaust.personHaroon, Mohamed
kaust.personShibl, Ahmed A.
kaust.personCahill, Matthew
kaust.personNgugi, David
kaust.personStingl, Ulrich
refterms.dateFOA2021-04-29T10:23:02Z
dc.date.published-online2019-06-17
dc.date.published-print2019-04-26


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