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Comprehensive Transcriptome Analysis Of Six Catfish Species From An Altitude Gradient Reveals Adaptive Evolution In Tibetan Fishes
Xiuhui Ma, Wei Dai, Jingliang Kang, Liandong Yang, Shunping He
Published 2015 · Biology, Medicine
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Glyptosternoid fishes (Siluriformes), one of the three broad fish lineages (the two other are schizothoracines and Triplophysa), have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes.
This paper references
Identification of an oxygen responsive enhancer element in the glyceraldehyde-3-phosphate dehydrogenase gene.
K. Graven (1999)
Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences.
N. Yu (2000)
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
J. Castresana (2000)
Gene array analysis and the liver
N. Shackel (2002)
Identification of an additional hypoxia responsive element in the glyceraldehyde-3-phosphate dehydrogenase gene promoter.
S. Lu (2002)
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis (2003)
Role of Ceruloplasmin in Macrophage Iron Efflux during Hypoxia*
J. Sarkar (2003)
Statistical significance for genomewide studies
John D. Storey (2003)
Statistical signi fi cance for genomewide studies
J. F. Storz (2003)
GeneWise and Genomewise.
E. Birney (2004)
Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data.
L. Rüber (2004)
Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences.
Xianguang Guo (2005)
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
Jianzhi Zhang (2005)
Phylogeny and biogeography of Chinese sisorid cat fi shes re - examined using mitochondrial cytochrome b and 16 S rRNA gene sequences
M. Goralska (2005)
The hepatic transcriptome in human liver disease
N. Shackel (2006)
The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells.
J. Mansfeld (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li (2006)
Uplift of the Tibetan plateau: evidence from divergence times of glyptosternoid catfishes.
Zuogang Peng (2006)
A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch
Vishal Saxena (2006)
Sterol Regulatory Element Binding Protein Is a Principal Regulator of Anaerobic Gene Expression in Fission Yeast
B. Todd (2006)
Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fi ssion yeast
R. C. Meister (2006)
Two routes to functional adaptation: Tibetan and Andean high-altitude natives
C. Beall (2007)
HEMOGLOBIN FUNCTION AND PHYSIOLOGICAL ADAPTATION TO HYPOXIA IN HIGH-ALTITUDE MAMMALS
J. F. Storz (2007)
PAML 4: phylogenetic analysis by maximum likelihood.
Ziheng Yang (2007)
Mechanisms of hemoglobin adaptation to high altitude hypoxia.
J. F. Storz (2008)
HaMStR: Profile hidden markov model based search for orthologs in ESTs
I. Ebersberger (2008)
High-throughput functional annotation and data mining with the Blast2GO suite
Stefan Götz (2008)
Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
M. Goodman (2009)
Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin
J. F. Storz (2009)
Optimization of de novo transcriptome assembly from next-generation sequencing data.
Y. Surget-Groba (2010)
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Xin Yi (2010)
Sterol Regulatory Element Binding Proteins in Fungi: Hypoxic Transcription Factors Linked to Pathogenesis
Clara M. Bien (2010)
Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders
C. Beall (2010)
Genetic differences in hemoglobin function between highland and lowland deer mice
J. F. Storz (2010)
Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
A. Bigham (2010)
De novo assembly and analysis of RNA-seq data
Gordon Robertson (2010)
Genetic Evidence for High-Altitude Adaptation in Tibet
T. Simonson (2010)
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
M. Grabherr (2011)
Cutadapt removes adapter sequences from high-throughput sequencing reads
Marcel Martin (2011)
Genetic variations in Tibetan populations and high-altitude adaptation at the Himalayas.
Yi Peng (2011)
Accelerated Profile HMM Searches
S. Eddy (2011)
De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification
Rohini Garg (2011)
Accelerated pro fi le HMM searches
R. Garg (2011)
Speciation: Clash of the Genomes
B. Harr (2012)
Expression and uptake of the thyroxine-binding protein transthyretin is regulated by oxygen in primary trophoblast placental cells.
J. Patel (2012)
The genomic basis of adaptive evolution in threespine sticklebacks
F. Jones (2012)
Ceruloplasmin alters intracellular iron regulated proteins and pathways: ferritin, transferrin receptor, glutamate and hypoxia-inducible factor-1α.
J. Harned (2012)
Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.
Baocheng Guo (2012)
The yak genome and adaptation to life at high altitude
Q. Qiu (2012)
Genomic divergence between nine- and three-spined sticklebacks
B. Guo (2013)
The genomic signature of dog domestication reveals adaptation to a starch-rich diet
E. Axelsson (2013)
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
M. Li (2013)
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Joana Projecto-Garcia (2013)
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
Chandrasekhar Natarajan (2013)
Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
Adam L Bazinet (2013)
Draft genome sequence of the Tibetan antelope
Ri-Li Ge (2013)
High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses.
Y. Li (2013)
Highly confined ions store charge more efficiently in supercapacitors.
C. Merlet (2013)
Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
Y. Qu (2013)
Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation
Shancen Zhao (2013)
Impaired Cytoplasmic–Nuclear Transport of Hypoxia‐Inducible Factor‐1α in Amyotrophic Lateral Sclerosis
Yuko Nagara (2013)
Impaired cytoplasmicnuclear transport of hypoxiainducible factor - 1 alpha in amyotrophic lateral sclerosis
R. E. Weber (2013)
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
S. Aflitos (2014)
Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One
J. V. Leuven (2014)
Genome evolution: Evolutionary insights from comparative bear genomics
Linda Koch (2014)
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang (2014)
Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus
L. Yang (2014)
Population variation revealed high-altitude adaptation of Tibetan mastiffs.
Y. Li (2014)
Differential regulation of GLUT1 and GLUT8 expression by hypoxia in mammary epithelial cells.
Y. Shao (2014)
Inhibitory effect of insulin-like growth factor-binding protein-7 (IGFBP7) on in vitro angiogenesis of vascular endothelial cells in the rat corpus luteum
K. Tamura (2014)
Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.
X. Gou (2014)
Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
V. Soria-Carrasco (2014)
Differential regulation of GLUT 1 and GLUT 8 expression by hypoxia in mammary epithelial cells
C. D. Huff (2014)
Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense
B. Joseph (2015)
in the analysis of the results. S.H. contributed to the research design and writing of the manuscript. All authors read and approved the final manuscript
Adaptive Evolution in Tibetan Fishes | 147
This paper is referenced by
Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau
Shi-Jun Xiao (2021)
Comparative transcriptomic analysis of fireflies (Coleoptera: Lampyridae) to explore the molecular adaptations to fresh water
Qi-Lin Zhang (2020)
De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus).
Fangfang Shen (2020)
Analysis of Multiplicity of Hypoxia-Inducible Factors in the Evolution of Triplophysa Fish (Osteichthyes: Nemacheilinae) Reveals Hypoxic Environments Adaptation to Tibetan Plateau
Juan Chen (2020)
Transcriptomic evidences of local thermal adaptation for the native fish Colossoma macropomum (Cuvier, 1818)
Luciana Mara Fé-Gonçalves (2020)
Integrated transcriptome provides resources and insights into the adaptive evolution of colonized brown trout (Salmo trutta fario) in the Tibetan Plateau
Xiaowen Chen (2020)
Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish.
Chao Tong (2020)
Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing
Y. Tuo (2020)
Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish
Chao Tong (2020)
Transcriptomics in aquaculture: current status and applications
Sathyajith Chandhini (2019)
Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp (Oratosquilla oratoria) under Thermal Stress
F. Lou (2019)
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
M. A. Bernal (2019)
Comparative genomics identifies rapidly evolving ion transport genes in a saline-alkaline lake-dwelling Schizothoracine fish
C. Tong (2019)
Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros
Chang-fei Guan (2019)
Comparative transcriptomics reveal that adaptive evolution in immune genes drives the local adaptation and speciation of schizothoracine fish
Delin Qi (2019)
Divergence, evolution and adaptation in ray-finned fish genomes
Chao Bian (2019)
Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives
Yan Hao (2019)
Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau
C. Tong (2019)
High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database.
Yunhai Yi (2019)
Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I.
Qingqing Wang (2018)
Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms
Gianni M. Castiglione (2018)
Author Correction: Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq
Jingliang Kang (2018)
Isolation and characterization of microsatellite markers in a highland fish, Pareuchiloglanis sinensis (Siluriformes: Sisoridae) by next-generation sequencing
W. Chen (2018)
Comparative transcriptomic analysis of Tibetan Gynaephora to explore the genetic basis of insect adaptation to divergent altitude environments
Q. Zhang (2017)
Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai–Tibetan Plateau
D. Zhang (2017)
Divergent adaptation to Qinghai-Tibetan Plateau implicated from transciptome study of Gymnocypris dobula and Schizothorax nukiangensis
Mengchao Yu (2017)
Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis
Jingliang Kang (2017)
Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq
Jingliang Kang (2017)
Global analysis of transcriptome sequences highlights accelerated evolution of immune genes in Danio choprae and Danio albolineatus
Lingsheng Bao (2017)
Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)
Shaokui Yi (2016)