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Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments
Wang, Yong1,2; Yang, Jiang Ke1; Lee, On On1; Li, Tie Gang3; Al-Suwailem, Abdulaziz3; Danchin, Antoine4,5; Qian, Pei-Yuan1
2011-12-21
Source PublicationPLOS ONE
Volume6Issue:12
SubtypeArticle
AbstractThe complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.
DOI10.1371/journal.pone.0029149
Indexed BySCI
Language英语
WOS IDWOS:000299113600060
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/32926
Collection实验海洋生物学重点实验室
Affiliation1.Hong Kong Univ Sci & Technol, Div Life Sci, KAUST Global Collaborat Res, Clear Water Bay, Hong Kong, Peoples R China
2.Chinese Acad Sci, Inst Oceanog, Qingdao, Peoples R China
3.King Abdullah Univ Sci & Technol, Thuwal, Saudi Arabia
4.SAS, AMAbiot, Evry, France
5.CEA Genoscope, Evry, France
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Wang, Yong,Yang, Jiang Ke,Lee, On On,et al. Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments[J]. PLOS ONE,2011,6(12).
APA Wang, Yong.,Yang, Jiang Ke.,Lee, On On.,Li, Tie Gang.,Al-Suwailem, Abdulaziz.,...&Qian, Pei-Yuan.(2011).Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments.PLOS ONE,6(12).
MLA Wang, Yong,et al."Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments".PLOS ONE 6.12(2011).
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