Online citations, reference lists, and bibliographies.
← Back to Search

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

Save to my Library
Download PDF
Analyze on Scholarcy Visualize in Litmaps
Share
Reduce the time it takes to create your bibliography by a factor of 10 by using the world’s favourite reference manager
Time to take this seriously.
Get Citationsy
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
10.1016/S0167-4781(99)00118-9
Identification of an oxygen responsive enhancer element in the glyceraldehyde-3-phosphate dehydrogenase gene.
K. Graven (1999)
10.1006/MPEV.2000.0776
Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences.
N. Yu (2000)
10.1093/OXFORDJOURNALS.MOLBEV.A026334
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
J. Castresana (2000)
10.1002/hep.1840360603
Gene array analysis and the liver
N. Shackel (2002)
10.1016/S0167-4781(01)00359-1
Identification of an additional hypoxia responsive element in the glyceraldehyde-3-phosphate dehydrogenase gene promoter.
S. Lu (2002)
10.1186/gb-2003-4-9-r60
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis (2003)
10.1074/jbc.M304926200
Role of Ceruloplasmin in Macrophage Iron Efflux during Hypoxia*
J. Sarkar (2003)
10.1073/pnas.1530509100
Statistical significance for genomewide studies
John D. Storey (2003)
Statistical signi fi cance for genomewide studies
J. F. Storz (2003)
10.1101/GR.1865504
GeneWise and Genomewise.
E. Birney (2004)
10.1016/J.YMPEV.2004.04.020
Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data.
L. Rüber (2004)
10.1016/J.YMPEV.2004.12.015
Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences.
Xianguang Guo (2005)
10.1093/MOLBEV/MSI237
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)
10.1186/1476-5926-5-6
The hepatic transcriptome in human liver disease
N. Shackel (2006)
10.1016/J.MOLCEL.2006.02.015
The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells.
J. Mansfeld (2006)
10.1093/bioinformatics/btl158
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li (2006)
10.1016/J.YMPEV.2005.10.016
Uplift of the Tibetan plateau: evidence from divergence times of glyptosternoid catfishes.
Zuogang Peng (2006)
10.1186/1471-2164-8-430
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)
10.1128/MCB.26.7.2817-2831.2006
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)
10.1073/pnas.0701985104
Two routes to functional adaptation: Tibetan and Andean high-altitude natives
C. Beall (2007)
10.1644/06-MAMM-S-199R1.1
HEMOGLOBIN FUNCTION AND PHYSIOLOGICAL ADAPTATION TO HYPOXIA IN HIGH-ALTITUDE MAMMALS
J. F. Storz (2007)
10.1093/MOLBEV/MSM088
PAML 4: phylogenetic analysis by maximum likelihood.
Ziheng Yang (2007)
10.1089/ham.2007.1079
Mechanisms of hemoglobin adaptation to high altitude hypoxia.
J. F. Storz (2008)
10.1186/1471-2148-9-157
HaMStR: Profile hidden markov model based search for orthologs in ESTs
I. Ebersberger (2008)
10.1093/nar/gkn176
High-throughput functional annotation and data mining with the Blast2GO suite
Stefan Götz (2008)
10.1073/pnas.0911239106
Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
M. Goodman (2009)
10.1073/pnas.0905224106
Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin
J. F. Storz (2009)
10.1101/gr.103846.109
Optimization of de novo transcriptome assembly from next-generation sequencing data.
Y. Surget-Groba (2010)
10.1126/science.1190371
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Xin Yi (2010)
10.1128/EC.00358-09
Sterol Regulatory Element Binding Proteins in Fungi: Hypoxic Transcription Factors Linked to Pathogenesis
Clara M. Bien (2010)
10.1073/pnas.1002443107
Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders
C. Beall (2010)
10.1242/jeb.042598
Genetic differences in hemoglobin function between highland and lowland deer mice
J. F. Storz (2010)
10.1371/journal.pgen.1001116
Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
A. Bigham (2010)
10.1038/nmeth.1517
De novo assembly and analysis of RNA-seq data
Gordon Robertson (2010)
10.1126/science.1189406
Genetic Evidence for High-Altitude Adaptation in Tibet
T. Simonson (2010)
10.1038/nbt.1883
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
M. Grabherr (2011)
10.14806/EJ.17.1.200
Cutadapt removes adapter sequences from high-throughput sequencing reads
Marcel Martin (2011)
10.1093/molbev/msq290
Genetic variations in Tibetan populations and high-altitude adaptation at the Himalayas.
Yi Peng (2011)
10.1371/journal.pcbi.1002195
Accelerated Profile HMM Searches
S. Eddy (2011)
10.1093/dnares/dsq028
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)
10.1016/j.cub.2012.11.005
Speciation: Clash of the Genomes
B. Harr (2012)
10.1530/JOE-11-0348
Expression and uptake of the thyroxine-binding protein transthyretin is regulated by oxygen in primary trophoblast placental cells.
J. Patel (2012)
10.1038/nature10944
The genomic basis of adaptive evolution in threespine sticklebacks
F. Jones (2012)
10.1016/j.exer.2012.02.001
Ceruloplasmin alters intracellular iron regulated proteins and pathways: ferritin, transferrin receptor, glutamate and hypoxia-inducible factor-1α.
J. Harned (2012)
10.1093/MOLBEV/MSS108
Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.
Baocheng Guo (2012)
10.1038/ng.2343
The yak genome and adaptation to life at high altitude
Q. Qiu (2012)
10.1186/1471-2164-14-756
Genomic divergence between nine- and three-spined sticklebacks
B. Guo (2013)
10.1038/nature11837
The genomic signature of dog domestication reveals adaptation to a starch-rich diet
E. Axelsson (2013)
10.1038/ng.2811
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
M. Li (2013)
10.1073/pnas.1315456110
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Joana Projecto-Garcia (2013)
10.1126/science.1236862
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
Chandrasekhar Natarajan (2013)
10.1371/journal.pone.0082615
Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
Adam L Bazinet (2013)
10.1038/ncomms2860
Draft genome sequence of the Tibetan antelope
Ri-Li Ge (2013)
10.1016/j.gene.2012.12.096
High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses.
Y. Li (2013)
10.1038/ncomms3701
Highly confined ions store charge more efficiently in supercapacitors.
C. Merlet (2013)
10.1038/ncomms3071
Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
Y. Qu (2013)
10.1038/ng.2494
Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation
Shancen Zhao (2013)
10.1111/bpa.12040
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)
10.1111/tpj.12616
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
S. Aflitos (2014)
10.1016/j.cell.2014.07.047
Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One
J. V. Leuven (2014)
10.1038/nrg3757
Genome evolution: Evolutionary insights from comparative bear genomics
Linda Koch (2014)
10.1126/science.1251385
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang (2014)
10.1093/gbe/evu279
Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus
L. Yang (2014)
10.1093/molbev/msu070
Population variation revealed high-altitude adaptation of Tibetan mastiffs.
Y. Li (2014)
10.1152/ajpregu.00093.2014
Differential regulation of GLUT1 and GLUT8 expression by hypoxia in mammary epithelial cells.
Y. Shao (2014)
10.1262/jrd.2014-069
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)
10.1101/gr.171876.113
Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.
X. Gou (2014)
10.1126/science.1252136
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)
10.1371/journal.pgen.1004779
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
10.24272/j.issn.2095-8137.2021.096
Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau
Shi-Jun Xiao (2021)
10.1111/mec.15504
Comparative transcriptomic analysis of fireflies (Coleoptera: Lampyridae) to explore the molecular adaptations to fresh water
Qi-Lin Zhang (2020)
10.1016/j.ygeno.2020.01.026
De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus).
Fangfang Shen (2020)
10.3389/fgene.2020.00433
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)
10.1590/1678-4685-GMB-2019-0377
Transcriptomic evidences of local thermal adaptation for the native fish Colossoma macropomum (Cuvier, 1818)
Luciana Mara Fé-Gonçalves (2020)
10.1111/JWAS.12621
Integrated transcriptome provides resources and insights into the adaptive evolution of colonized brown trout (Salmo trutta fario) in the Tibetan Plateau
Xiaowen Chen (2020)
10.1016/j.ijbiomac.2020.01.207
Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish.
Chao Tong (2020)
10.3389/fgene.2020.00714
Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing
Y. Tuo (2020)
10.1101/825885
Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish
Chao Tong (2020)
10.1111/RAQ.12298
Transcriptomics in aquaculture: current status and applications
Sathyajith Chandhini (2019)
10.3390/ani9070399
Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp (Oratosquilla oratoria) under Thermal Stress
F. Lou (2019)
10.7717/peerj.6541
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
M. A. Bernal (2019)
10.1101/825885
Comparative genomics identifies rapidly evolving ion transport genes in a saline-alkaline lake-dwelling Schizothoracine fish
C. Tong (2019)
10.1186/s12870-019-1839-2
Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros
Chang-fei Guan (2019)
10.1101/714881
Comparative transcriptomics reveal that adaptive evolution in immune genes drives the local adaptation and speciation of schizothoracine fish
Delin Qi (2019)
10.1007/s11427-018-9499-5
Divergence, evolution and adaptation in ray-finned fish genomes
Chao Bian (2019)
10.1073/pnas.1819657116
Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives
Yan Hao (2019)
10.1101/813501
Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau
C. Tong (2019)
10.1016/j.ygeno.2018.11.023
High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database.
Yunhai Yi (2019)
10.1016/j.cbd.2018.06.002
Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I.
Qingqing Wang (2018)
10.1111/evo.13396
Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms
Gianni M. Castiglione (2018)
10.1038/s41598-018-27677-7
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)
10.1007/s12041-018-0997-6
Isolation and characterization of microsatellite markers in a highland fish, Pareuchiloglanis sinensis (Siluriformes: Sisoridae) by next-generation sequencing
W. Chen (2018)
10.1038/s41598-017-17051-4
Comparative transcriptomic analysis of Tibetan Gynaephora to explore the genetic basis of insect adaptation to divergent altitude environments
Q. Zhang (2017)
10.1534/g3.116.038406
Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai–Tibetan Plateau
D. Zhang (2017)
10.1016/J.BSE.2017.02.003
Divergent adaptation to Qinghai-Tibetan Plateau implicated from transciptome study of Gymnocypris dobula and Schizothorax nukiangensis
Mengchao Yu (2017)
10.1186/s12862-017-1074-0
Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis
Jingliang Kang (2017)
10.1038/s41598-017-02853-3
Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq
Jingliang Kang (2017)
10.1016/j.fsi.2017.05.011
Global analysis of transcriptome sequences highlights accelerated evolution of immune genes in Danio choprae and Danio albolineatus
Lingsheng Bao (2017)
10.3390/ijms17121943
Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)
Shaokui Yi (2016)
Semantic Scholar Logo Some data provided by SemanticScholar