The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau
Crabbe, M. James C.
Qinghai Nationalities University
Chinese Academy of Sciences
University of Oxford
University of Bedfordshire
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AbstractThe Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP.
CitationQiao Q, Huang YY, Qi J, Qu MZ, Jiang C, Lin PC, Li RH, Song LR, Yonezawa T, Hasegawa M, Crabbe MJC, Chen F, Zhang TC, Zhong Y (2016) 'The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau', Scientific Reports, 6.
PublisherNATURE PUBLISHING GROUP
PubMed Central IDPMC4933973
SponsorsWe thank Xiaoni Gan for suggestions to improve the manuscript. This work is supported by grants from National Natural Science Foundation of China (91131901, 31300201, 31590820, 31590823), National High Technology Research and Development Program of China (2014AA020528), the specimen platform of China and the PSCIRT project.
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