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

Walworth Nathan; Pfreundt Ulrike; Nelson William C.Mincer TracyHeidelberg John F.Fu FeixueWaterbury John B.del Rio Tijana GlavinaGoodwin LynneKyrpides Nikos C.Land Miriam L.Woyke TanjaHutchins David A.Hess Wolfgang R.Webb Eric A.

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

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

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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. 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 caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. 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.

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《Proceedings of the National Academy of Sciences of the United States of America》 |2015年第14期|4251-4256|共6页
作者
Walworth Nathan; Pfreundt Ulrike; Nelson William C.Mincer TracyHeidelberg John F.Fu FeixueWaterbury John B.del Rio Tijana GlavinaGoodwin LynneKyrpides Nikos C.Land Miriam L.Woyke TanjaHutchins David A.Hess Wolfgang R.Webb Eric A.;
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作者单位

Woods Hole Oceanog Inst, Dept Marine Chem & Geochem, Woods Hole, MA 02543 USA;

Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA;

Woods Hole Oceanog Inst, Dept Biol, Woods Hole, MA 02543 USAJoint Genome Inst, Walnut Creek, CA 94598 USAOak Ridge Natl Lab, Oak Ridge, TN 37831 USAUniv Freiburg, Genet & Expt Bioinformat, D-79098 Freiburg, GermanyPacific NW Natl Lab, Fundamental & Computat Sci, Richland, WA 99352 USA;

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收录信息美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
原文格式 PDF
正文语种英语
中图分类自然科学总论;
关键词
marine microbiology; oligotrophic; evolution genomics; nitrogen fixation;

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

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