The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

2.50
Hdl Handle:
http://hdl.handle.net/10547/622009
Title:
The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau
Authors:
Qiao, Qin; Huang, Yanyan; Qi, Ji.; Qu, Mingzhi; Jiang, Chen; Lin, Pengcheng; Li, Renhui; Song, Lirong; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C.; Chen, Fan; Zhang, Ti-Cao; Zhong, Yang
Abstract:
The 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.
Affiliation:
Fudan University; Tibet University; Yunnan University; Qinghai Nationalities University; Chinese Academy of Sciences; University of Oxford; University of Bedfordshire
Citation:
Qiao 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.
Publisher:
NATURE PUBLISHING GROUP
Journal:
Scientific Reports
Issue Date:
6-Jul-2016
URI:
http://hdl.handle.net/10547/622009
DOI:
10.1038/srep29404
Additional Links:
http://www.nature.com/articles/srep29404
Type:
Article
Language:
en
ISSN:
2045-2322
Sponsors:
We 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.
Appears in Collections:
Biomedical and biological science

Full metadata record

DC FieldValue Language
dc.contributor.authorQiao, Qinen
dc.contributor.authorHuang, Yanyanen
dc.contributor.authorQi, Ji.en
dc.contributor.authorQu, Mingzhien
dc.contributor.authorJiang, Chenen
dc.contributor.authorLin, Pengchengen
dc.contributor.authorLi, Renhuien
dc.contributor.authorSong, Lirongen
dc.contributor.authorYonezawa, Takahiroen
dc.contributor.authorHasegawa, Masamien
dc.contributor.authorCrabbe, M. James C.en
dc.contributor.authorChen, Fanen
dc.contributor.authorZhang, Ti-Caoen
dc.contributor.authorZhong, Yangen
dc.date.accessioned2017-01-30T11:48:38Z-
dc.date.available2017-01-30T11:48:38Z-
dc.date.issued2016-07-06-
dc.identifier.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.en
dc.identifier.issn2045-2322-
dc.identifier.doi10.1038/srep29404-
dc.identifier.urihttp://hdl.handle.net/10547/622009-
dc.description.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.en
dc.description.sponsorshipWe 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.en
dc.language.isoenen
dc.publisherNATURE PUBLISHING GROUPen
dc.relation.urlhttp://www.nature.com/articles/srep29404en
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF-
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectcyanobacteriaen
dc.subjectgeneticsen
dc.subjecttranscriptomeen
dc.subjectC400 Geneticsen
dc.titleThe genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateauen
dc.typeArticleen
dc.contributor.departmentFudan Universityen
dc.contributor.departmentTibet Universityen
dc.contributor.departmentYunnan Universityen
dc.contributor.departmentQinghai Nationalities Universityen
dc.contributor.departmentChinese Academy of Sciencesen
dc.contributor.departmentUniversity of Oxforden
dc.contributor.departmentUniversity of Bedfordshireen
dc.identifier.journalScientific Reportsen
dc.date.updated2017-01-30T11:31:08Z-
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