PUBLICATION

Evidence for adaptation to the Tibetan Plateau inferred from Tibetan loach transcriptomes

Authors
Wang, Y., Yang, L., Zhou, K., Zhang, Y., Song, Z., He, S.
ID
ZDB-PUB-151011-1
Date
2015
Source
Genome biology and evolution   7(11): 2970-82 (Journal)
Registered Authors
Keywords
Tibetan Plateau, Triplophysa fishes, accelerated evolution, adaptation, transcriptome
MeSH Terms
  • Adaptation, Physiological/genetics*
  • Altitude*
  • Amino Acid Sequence
  • Animals
  • Aryl Hydrocarbon Receptor Nuclear Translocator/genetics
  • Bayes Theorem
  • Biological Evolution*
  • China
  • Cypriniformes/genetics
  • Cypriniformes/physiology*
  • Energy Metabolism/genetics
  • Fishes/genetics
  • Fishes/physiology
  • Hypoxia/genetics
  • Hypoxia-Inducible Factor 1, alpha Subunit/genetics
  • Likelihood Functions
  • Male
  • Models, Genetic
  • Molecular Sequence Data
  • Mutation
  • Phylogeny
  • Selection, Genetic
  • Sequence Analysis, RNA
  • Transcriptome*
PubMed
26454018 Full text @ Genome Biol. Evol.
Abstract
Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, i.e., Triplophysa siluroides, T. scleroptera, and T. dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus) and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping