Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jul 6:6:29404.
doi: 10.1038/srep29404.

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

Qin Qiao  1   2 , Yanyan Huang  1 , Ji Qi  1 , Mingzhi Qu  1 , Chen Jiang  1 , Pengcheng Lin  3 , Renhui Li  4 , Lirong Song  4 , Takahiro Yonezawa  1 , Masami Hasegawa  1 , M James C Crabbe  5   6 , Fan Chen  7 , Ticao Zhang  8 , Yang Zhong  9   1
Affiliations

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

Qin Qiao et al. Sci Rep. .

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Comparative genomic analysis between T. sp. NMC-1 and close relatives.
(A) comparison of COG functional classification among the seven relatives. (B) The significantly (P < 0.05) expanded and contracted COG clusters in T. sp. NMC-1 compared with the six close relatives. (C) Comparison of orthogroups among the four closest relatives.
Figure 2
Figure 2. Phylogenomics of the Cyanobacteria phylum as determined using CVTree software.
Figure 3
Figure 3
The most significantly (P < 0.0001) expanded (A) and contracted (B) COG clusters in T. sp. NMC-1 genome compared to six close relatives.
Figure 4
Figure 4. COG enrichment analysis of species-specific genes, differentially expressed genes and positively selected genes in T. sp. NMC-1.
Figure 5
Figure 5. Positive selection analysis of O-methyltransferase in T. sp. NMC-1.
(A) Multiple sequence alignment of O-methyltransferase. (B) Positive selection test of seven relatives using the branch-site model in the PAML 4 package. (C) Predicted three-dimensional structure of O-methyltransferase in T. sp. NMC-1. The positive-selection site (Asn-109) is labeled.
See this image and copyright information in PMC

References

    1. Myers N., Mittermeier R. A., Mittermeier C. G., Da Fonseca G. A. & Kent J. Biodiversity hotspots for conservation priorities. Nature 403, 853–858 (2000). - PubMed
    1. Cheviron Z. A. & Brumfield R. T. Genomic insights into adaptation to high-altitude environments. Heredity 108, 354–361 (2012). - PMC - PubMed
    1. Qiu Q. et al.. The yak genome and adaptation to life at high altitude. Nature Genetics 44, 946–949 (2012). - PubMed
    1. Qu Y. et al.. Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Communications 4 (2013). - PubMed
    1. Li M. et al.. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nature Genetics 45, 1431–1438 (2013). - PubMed

Publication types

Substances

LinkOut - more resources