title: The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau.
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.
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.|School of Agriculture, Yunnan University, Kunming, 650091, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Qiao
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Qi
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Qu
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Jiang
authors.affiliation: College of Chemistry and Life Sciences, Qinghai University for Nationalities, Xining, 810007, China.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Lin
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Renhui
authors.initials: R
authors.lastname: Li
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
authors.forename: Lirong
authors.initials: L
authors.lastname: Song
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Yonezawa
authors.affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Masami
authors.initials: M
authors.lastname: Hasegawa
authors.affiliation: Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.|Institute of Biomedical and Environmental Science &Technology, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.
authors.forename: M James C
authors.initials: MJ
authors.lastname: Crabbe
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Chen
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China.
authors.forename: Ticao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa, 850012, China.|Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhong
mesh_terms: D000220:Adaptation, Biological; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D003080:Cold Temperature; D000458:Cyanobacteria / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling / Q000379:methods*; D059646:Genome Size; D016680:Genome, Bacterial; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA; D018609:Tibet
chemical_list: D001426:Bacterial Proteins