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Title: Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20–25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. In this paper, we use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift causedmore » by periodic blooms of a subset of genotypes, which may have reduced effective population size. Finally, our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual “inflation” of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [1] ;  [1] ;  [5] ;  [6] ;  [6] ;  [6] ;  [7] ;  [6] ;  [1] ;  [2] ;  [1]
  1. Univ. of Southern California, Los Angeles, CA (United States). Dept. of Biological Sciences
  2. Univ. of Freiburg (Germany). Genetics and Experiment Bioinformatics
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Fundamental and Computational Sciences
  4. Woods Hole Oceanographic Inst., Woods Hole, MA (United States). Marine Chemistry and Geochemistry Dept.
  5. Woods Hole Oceanographic Inst., Woods Hole, MA (United States). Biology Dept.
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
OSTI Identifier:
1286733
Grant/Contract Number:
AC02-05CH11231; AC03-76SF00098
Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 112; Journal Issue: 14; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Research Org:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Contributing Orgs:
Univ. of Southern California, Los Angeles, CA (United States); Woods Hole Oceanographic Inst., Woods Hole, MA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES marine biology; oligotrophic; evolution genomics; nitrogen fixation