Sire JY, Akimenko MA. Scale development in fish: a review, with description of sonic hedgehog (shh) expression in the zebrafish (Danio rerio). Int J Dev Biol. 2003;48:233–47.
Article
Google Scholar
Zhu D, Ortega CF, Motamedi R, Szewciw L, Vernerey F, Barthelat F. Structure and mechanical performance of a “modern” fish scale. Adv Eng Mater. 2012;14:B185–94.
Article
Google Scholar
Yang W, Gludovatz B, Zimmermann EA, Bale HA, Ritchie RO, Meyers MA. Structure and fracture resistance of alligator gar (Atractosteus spatula) armored fish scales. Acta Biomater. 2013;9:5876–89.
Article
CAS
PubMed
Google Scholar
Franklin DR, Smith LL Jr. Note on development of scale patterns in the northern pike, Esox lucius L. T. Am Fish Soc. 1960;89:83.
Article
Google Scholar
McCrimmon HR, Swee UB. Scale formation as related to growth and development of young carp, Cyprinus carpio L. J Fish Res Bd Can. 1967;24:47–51.
Article
Google Scholar
Sire JY, Quilhac A, Bourguignon J, Allizard F. Evidence for participation of the epidermis in the deposition of superficial layer of scales in zebrafish (Danio rerio): a SEM and TEM study. J Morphol. 1997;231:161–74.
Article
PubMed
Google Scholar
Yan TM, Tang RJ, Liu XS, Yang SY, Yang S, He Z. The scale formation and development in juvenile of Schizothorax prenanti. Acta Hydrob Sin. 2014;38:298–303.
Google Scholar
Sharpe PT. Fish scale development: hair today, teeth and scales yesterday? Curr Biol. 2001;11:R751–2.
Article
CAS
PubMed
Google Scholar
Kondo S, Kuwahara Y, Kondo M, Naruse K, Mitani H, Wakamatsu Y, Ozato K, Asakawa S, Shimizu N, Shima A. The medaka rs-3 locus required for scale development encodes ectodysplasin-a receptor. Curr Biol. 2001;11:1202–6.
Article
CAS
PubMed
Google Scholar
Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun. 2016;7:11757.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lv Y, Kawasaki K, Li J, Li Y, Bian C, Huang Y, You X, Shi Q. A genomic survey of SCPP family genes in fishes provides novel insights into the evolution of fish scales. Int J Mol Sci. 2017;18:2432.
Article
PubMed Central
CAS
Google Scholar
Zhang C, Tong C, Ludwig A, Tang Y, Liu S, Zhang R, Feng C, Li G, Peng Z, Zhao K. Adaptive evolution of the Eda gene and scales loss in schizothoracine fishes in response to uplift of the Tibetan plateau. Int J Mol Sci. 2018;19:2953.
Article
PubMed Central
CAS
Google Scholar
Qian X, Ba Y, Zhuang Q, Zhong G. RNA-Seq technology and its application in fish transcriptomics. OMICS. 2014;18:98–110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu B, Wang X, Feng X, Yu X, Tong J. Comparative transcriptomic analyses of two bighead carp (Hypophthalmichthys nobilis) groups with different growth rates. Comp Biochem Physiol D. 2016;20:111–7.
CAS
Google Scholar
Bar I, Cummins S, Elizur A. Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the southern bluefin tuna (Thunnus maccoyii). BMC Genomics. 2016;17:217.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang X, Wang S, Chen S, Chen Y, Liu Y, Shao C, Wang Q, Lu Y, Gong G, Ding S, et al. Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection. Fish Shellfish Immunol. 2015;43:209–18.
Article
CAS
PubMed
Google Scholar
Zhu W, Wang L, Dong Z, Chen X, Song F, Liu N, Yang H, Fu J. Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia. Sci Rep. 2016;6:31347.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen YF, Cao WX. Schizothoracinae. In: Yue P, editor. Fauna Sinica, Osteichthyes, Cypriniformes III. Beijing: Science Press; 2000. p. 273–335.
Google Scholar
Cao WX, Chen YY, Wu YF, Zhu SQ. Origin and evolution of schizothoracine fishes in relation to the upheaval of the Xizang Plateau. In: The team of the comprehensive scientific expedition to the Qinghai-Xizang Plateau, Chinese Academy of Sciences, editor. Studies on the period, amplitude and type of the uplift of the Qinghai-Xizang Plateau. Beijing: Science Press; 1981. p. 118–30.
Google Scholar
He D, Chen Y. Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences. J Biogeogr. 2006;33:1448–60.
Article
Google Scholar
Liang Y, He D, Jia Y, Sun H, Chen Y. Phylogeographic studies of schizothoracine fishes on the Central Qinghai-Tibet plateau reveal the highest known glacial microrefugia. Sci Rep. 2017;7:10983.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tao J, He D, Kennard MJ, Ding C, Bunn SE, Liu C, Jia Y, Che R, Chen Y. Strong evidence for changing fish reproductive phenology under climate warming on the Tibetan plateau. Glob Chang Biol. 2018;24:2093–104.
Article
PubMed
Google Scholar
Feng X, Jia Y, Zhu R, Chen K, Chen Y. Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan plateau using single-molecule long-read sequencing and RNA-seq. DNA Res. 2019;26:353–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512.
Article
CAS
PubMed
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qi D, Chao Y, Wu R, Xia M, Chen Q, Zheng Z. Transcriptome analysis provides insights into the adaptive responses to hypoxia of a schizothoracine fish (Gymnocypris eckloni). Front Physiol. 2018;9:1326.
Article
PubMed
PubMed Central
Google Scholar
Li S. The scale formation process and its relation to the growth of five species of fish. J Fish China. 1983;7:343–51.
Google Scholar
Sire JY, Arnulf I. Structure and development of the ctenial spines on the scales of a teleost fish, the cichlid Cichlasoma nigrofasciatum. Acta Zool. 2000;81:139–58.
Article
Google Scholar
White DS. Early development and pattern of scale formation in the spotted sucker, Minytrema melanops (Catostomidae). Copeia. 1977;1977:400–3.
Article
Google Scholar
Yu X, Li Y, Zhou T. Karyotype studies of cyprinid fishes in China: comparative study of the karyotypes of 8 species of schizothoracine fishes. J Wuhan Univ. 1990;02:97–104 (In Chinese).
Google Scholar
Liu HP, Xiao SJ, Wu N, Wang D, Liu YC, Zhou CW, Liu Q, Yang R, Jiang WK, Liang QQ, et al. The sequence and de novo assembly of Oxygymnocypris stewartii genome. Sci Data. 2019;6:190009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shimizu J, Asami N, Kataoka A, Sugihara F, Inoue N, Kimira Y, Wada M, Mano H. Oral collagen-derived dipeptides, prolyl-hydroxyproline and hydroxyprolyl-glycine, ameliorate skin barrier dysfunction and alter gene expression profiles in the skin. Biochem Bioph Res Co. 2015;456:626–30.
Article
CAS
Google Scholar
Montfort J, Le Cam A, Gabillard JC, Rescan PY. Gene expression profiling of trout regenerating muscle reveals common transcriptional signatures with hyperplastic growth zones of the post-embryonic myotome. BMC Genomics. 2016;17:810.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li RW, Schroeder SG. Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection. Funct Integr Genomic. 2012;12:35–44.
Article
CAS
Google Scholar
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010;18:662–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Cui X, Shen Y, Pang L, Zhang A, Fu Z, Chen J, Guo X, Gan W, Ji C. Distinct expression profiles of LncRNAs between brown adipose tissue and skeletal muscle. Biochem Bioph Res Co. 2014;443:1028–34.
Article
CAS
Google Scholar
Aubin JE, Liu F, Malaval L, Gupta AK. Osteoblast and chondroblast differentiation. Bone. 1995;17:S77–83.
Article
Google Scholar
Knopf F, Hammond C, Chekuru A, Kurth T, Hans S, Weber CW, Mahatma G, Fisher S, Brand M, Schulte-Merker S, et al. Bone regenerates via dedifferentiation of osteoblasts in the zebrafish fin. Dev Cell. 2011;20:713–24.
Article
CAS
PubMed
Google Scholar
Nishimoto SK, Waite JH, Nishimoto M, Kriwacki RW. Structure, activity, and distribution of fish osteocalcin. J Biol Chem. 2003;278:11843–8.
Article
CAS
PubMed
Google Scholar
Sire JY, Allizard F, Babiar O, Bourguignon J, Quilhac A. Scale development in zebrafish (Danio rerio). J Anat. 1997;190:545–61.
Article
PubMed
PubMed Central
Google Scholar
Metz JR, De Vrieze E, Lock EJ, Schulten IE, Flik G. Elasmoid scales of fishes as model in biomedical bone research. J Appl Ichthyol. 2012;28:382–7.
Article
Google Scholar
Feng X, He D, Shan G, Tao J, Chen Y. Integrated analysis of mRNA and miRNA expression profiles in Ptychobarbus dipogon and Schizothorax oconnori, insight into genetic mechanisms of high altitude adaptation in the schizothoracine fishes. Gene Rep. 2017;9:74–80.
Article
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
CAS
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK, Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–8.
Article
CAS
PubMed
Google Scholar