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Genetic signals of high-altitude adaptation in amphibians : A comparative transcriptome analysis

Yang, Weizhao LU ; Qi, Yin and Fu, Jinzhong (2016) In BMC Genetics 17(1).
Abstract

Background: High-altitude adaptation provides an excellent system for studying how organisms cope with multiple environmental stressors and interacting genetic modifications. To explore the genetic basis of high-altitude adaptation in poikilothermic animals, we acquired transcriptome sequences from a high-altitude population and a low-altitude population of the Asiatic toad (Bufo gargarizans). Transcriptome data from another high-altitude amphibian, Rana kukunoris and its low-altitude relative R. chensiensis, which are from a previous study, were also incorporated into our comparative analysis. Results: More than 40,000 transcripts were obtained from each transcriptome, and 5107 one-to-one orthologs were identified among the four taxa... (More)

Background: High-altitude adaptation provides an excellent system for studying how organisms cope with multiple environmental stressors and interacting genetic modifications. To explore the genetic basis of high-altitude adaptation in poikilothermic animals, we acquired transcriptome sequences from a high-altitude population and a low-altitude population of the Asiatic toad (Bufo gargarizans). Transcriptome data from another high-altitude amphibian, Rana kukunoris and its low-altitude relative R. chensiensis, which are from a previous study, were also incorporated into our comparative analysis. Results: More than 40,000 transcripts were obtained from each transcriptome, and 5107 one-to-one orthologs were identified among the four taxa for comparative analysis. A total of 29 (Bufo) and 33 (Rana) putative positively selected genes were identified for the two high-altitude species, which were mainly concentrated in nutrient metabolism related functions. Using SNP-tagging and FST outlier analysis, we further tested 89 other nutrient metabolism related genes for signatures of natural selection, and found that two genes, CAPN2 and ITPR1, were likely under balancing selection. We did not detect any positively selected genes associated with response to hypoxia. Conclusions: Amphibians clearly employ different genetic mechanisms for high-altitude adaptation compared to endotherms. Modifications of genes associated with nutrient metabolism feature prominently while genes related to hypoxia tolerance appear to be insignificant. Poikilotherms represent the majority of animal diversity, and we hope that our results will provide useful directions for future studies of amphibians as well as other poikilotherms.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Amphibians, Asiatic toads, Comparative analysis, F outlier analysis, High altitude, Nutrient metabolism, Positive selection, Transcriptome
in
BMC Genetics
volume
17
issue
1
publisher
BioMed Central
external identifiers
  • Scopus:84989341548
  • WOS:000385049900002
ISSN
1471-2156
DOI
10.1186/s12863-016-0440-z
language
English
LU publication?
yes
id
f0771143-f160-46e8-83c0-c9eb4dc374f9
date added to LUP
2016-10-14 11:47:28
date last changed
2017-01-14 03:00:13
@article{f0771143-f160-46e8-83c0-c9eb4dc374f9,
  abstract     = {<p>Background: High-altitude adaptation provides an excellent system for studying how organisms cope with multiple environmental stressors and interacting genetic modifications. To explore the genetic basis of high-altitude adaptation in poikilothermic animals, we acquired transcriptome sequences from a high-altitude population and a low-altitude population of the Asiatic toad (Bufo gargarizans). Transcriptome data from another high-altitude amphibian, Rana kukunoris and its low-altitude relative R. chensiensis, which are from a previous study, were also incorporated into our comparative analysis. Results: More than 40,000 transcripts were obtained from each transcriptome, and 5107 one-to-one orthologs were identified among the four taxa for comparative analysis. A total of 29 (Bufo) and 33 (Rana) putative positively selected genes were identified for the two high-altitude species, which were mainly concentrated in nutrient metabolism related functions. Using SNP-tagging and F<sub>ST</sub> outlier analysis, we further tested 89 other nutrient metabolism related genes for signatures of natural selection, and found that two genes, CAPN2 and ITPR1, were likely under balancing selection. We did not detect any positively selected genes associated with response to hypoxia. Conclusions: Amphibians clearly employ different genetic mechanisms for high-altitude adaptation compared to endotherms. Modifications of genes associated with nutrient metabolism feature prominently while genes related to hypoxia tolerance appear to be insignificant. Poikilotherms represent the majority of animal diversity, and we hope that our results will provide useful directions for future studies of amphibians as well as other poikilotherms.</p>},
  articleno    = {134},
  author       = {Yang, Weizhao and Qi, Yin and Fu, Jinzhong},
  issn         = {1471-2156},
  keyword      = {Amphibians,Asiatic toads,Comparative analysis,F outlier analysis,High altitude,Nutrient metabolism,Positive selection,Transcriptome},
  language     = {eng},
  month        = {10},
  number       = {1},
  publisher    = {BioMed Central},
  series       = {BMC Genetics},
  title        = {Genetic signals of high-altitude adaptation in amphibians : A comparative transcriptome analysis},
  url          = {http://dx.doi.org/10.1186/s12863-016-0440-z},
  volume       = {17},
  year         = {2016},
}