References
Abrusan G, Grundmann N, DeMester L, Makalowski W. 2009. TEclass–a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25:1329-1330.
Altschul S. 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215:403-410.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
An Z, Wang P, Shen J, Zhang Y, Zhang P, Wang S, Li X, Sun Q, Song Y, Al L, et al. 2006. Geophysical survey on the tectonic and sediment distribution of Qinghai Lake basin. Science in China Series D: Earth Sciences 49:851-861.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
Beier S, Thiel T, Munch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583-2585.
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31:1119-1125.
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552.
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884-i890.
Cui B-L, Li X-Y, Wei X-H. 2016. Isotope and hydrochemistry reveal evolutionary processes of lake water in Qinghai Lake. Journal of Great Lakes Research 42:580-587.
Ding L, Xu Q, Yue Y, Wang H, Cai F, Li S. 2014. The Andean-type Gangdese Mountains: Paleoelevation record from the Paleocene–Eocene Linzhou Basin. Earth planet. sc. lett. 392:250-264.
Ellis AE. 2001. Innate host defense mechanisms of fish against viruses and bacteria. Developmental & Comparative Immunology 25:827-839.
Fang X, Garzione C, Van der Voo R, Li J, Fan M. 2003. Flexural subsidence by 29 Ma on the NE edge of Tibet from the magnetostratigraphy of Linxia Basin, China. Earth and Planetary Science Letters 210:545-560.
Fu C, An Z, Qiang X, Bloemendal J, Song Y, Chang H. 2013. Magnetostratigraphic determination of the age of ancient Lake Qinghai, and record of the East Asian monsoon since 4.63 Ma. Geology 41:875-878.
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Jr., Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, et al. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31:5654-5666.
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9:R7.
Han J, Shao Z, Zhu D, Meng X, Yu J, Wang J, Lv R, Qian C, He C. 2013. Characteristics of river terraces and formation of the Yellow River in the source region of Yellow River. Geology in China 40:1531-1541.
Harrison TM, Copeland P, Kidd WS, Yin A. 1992. Raising tibet. Science 255:1663-1670.
Hoff KJ, Stanke M. 2019. Predicting Genes in Single Genomes with AUGUSTUS. Curr Protoc Bioinformatics 65:e57.
Hu J, Fan J, Sun Z, Liu S. 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253-2255.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. 2009. InterPro: the integrative protein signature database. Nucleic Acids Res 37:D211-215.
Jiang Z, Jiang J, Wang Y, Zhang E, Zhang Y, Li L, Xie F, Cai B, Cao L, Zhang G. 2016. Red List of China’s Vertebrates. Biodiversity Science 24:500-551.
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462-467.
Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772-780.
Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F. 2016. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res 44:e89.
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359.
Leggatt RA, Iwama GK. 2003. Occurrence of polyploidy in the fishes. Reviews in Fish Biology and Fisheries 13:237-246.
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094-3100.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
Li J. 1991. The environmental effects of the uplift of the Qinghai-Xizang Plateau. Quaternary Science Reviews 10:479-483.
Li L, Stoeckert CJ, Jr., Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178-2189.
Li Y, Ren Z, Shedlock AM, Wu J, Sang L, Tersing T, Hasegawa M, Yonezawa T, Zhong Y. 2013. High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses. Gene 517:169-178.
Liu B, Shi Y, Yuan J, Hu X, Zhang H, Li N, Li Z, Chen Y, Mu D, Fan W. 2013. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Quantitative Biology.
Magnadottir B. 2010. Immunological control of fish diseases. Mar Biotechnol (NY) 12:361-379.
Magnadottir B. 2006. Innate immunity of fish (overview). Fish Shellfish Immunology 20:137-151.
Molnar P, Boos WR, Battisti DS. 2010. Orographic controls on climate and paleoclimate of Asia: Thermal and mechanical roles for the Tibetan Plateau. Annual Review of Earth and Planetary Sciences 38:77-102.
Molnar P, England P, Martinod J. 1993. Mantle dynamics, uplift of the Tibetan Plateau, and the Indian Monsoon. Reviews of Geophysics 31.
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11:1650-1667.
Pryszcz LP, Gabaldon T. 2016. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Res 44:e113.
Shi Y, Li J, Li B, Yao T, Wang SL, Shijie, Cui Z, Wang F, Pan B, Fang X, Zhang Q. 1999. Uplift of the Qinghai-Xizang (Tibetan) plateau and East Asia environmental change during late cenozoic. Journal of Geographical Sciences 54:12-22.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210-3212.
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
Stanke M, Diekhans M, Baertsch R, Haussler D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637-644.
Tapponnier P, Zhiqin X, Roger F, Meyer B, Arnaud N, Wittlinger G, Jingsui Y. 2001. Oblique stepwise rise and growth of the Tibet plateau. Science 294:1671-1677.
Tian F, Liu S, Shi J, Qi H, Zhao K, Xie B. 2019. Transcriptomic profiling reveals molecular regulation of seasonal reproduction in Tibetan highland fish, Gymnocypris przewalskii. BMC Genomics 20:2.
Tong C, Li M. 2020. Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish. International Journal of Biological Macromolecules 149:341-347.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963.
Walker KF, Dunn IG, Edwards D, Petr T, Yang HZ. 1995. A fishery in a changing lake environment: The naked carp Gymnocypris przewalskii (Kessler) (Cyprinidae: schizothoracinae) in Qinghai Hu, China. International Journal of Salt Lake Research 4:169-222.
Wang C, Dai J, Zhao X, Li Y, Graham SA, He D, Ran B, Meng J. 2014. Outward-growth of the Tibetan Plateau during the Cenozoic: A review. Tectonophysics 621:1-43.
Wang S, Xie Y. 2009. China species red list: Higher education press, Beijing.
Wang X, Gan X, Li J, Chen Y, He S. 2016. Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau. Sci China Life Sci 59:1149-1165.
Wang YS, Gonzalez RJ, Patrick ML, Grosell M, Zhang C, Feng Q, Du J, Walsh PJ, Wood CM. 2003. Unusual physiology of scale-less carp, Gymnocypris przewalskii, in Lake Qinghai: a high altitude alkaline saline lake. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 134:409-421.
Whyte SK. 2007. The innate immune response of finfish–a review of current knowledge. Fish Shellfish Immunol 23:1127-1151.
Wood CM, Du J, Rogers J, Brauner CJ, Richards JG, Semple JW, Murray BW, Chen XQ, Wang Y. 2007. Przewalski’s naked carp (Gymnocypris przewalskii ): an endangered species taking a metabolic holiday in Lake Qinghai, China. Physiological and biochemical zoology 80:59-77.
Xiong F, Chen D, Duan X. 2010. Threatened fishes of the world: Gymnocypris przewalskii (Kessler, 1876) (Cyprinidae: Schizothoracinae). Environmental Biology of Fishes 87:351-352.
Xu H, Hou Z, An Z, Liu X, Dong J. 2010. Major ion chemistry of waters in Lake Qinghai catchments, NE Qinghai-Tibet plateau, China. Quaternary International 212:35-43.
Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.
Yao Z, Guo W, Lai Q, Shi J, Zhou K, Qi H, Lin T, Li Z, Wang H. 2016. Gymnocypris przewalskiidecreases cytosolic carbonic anhydrase expression to compensate for respiratory alkalosis and osmoregulation in the saline-alkaline lake Qinghai. Journal of Comparative Physiology B 186:83-95.
Yin A, Harrison TM. 2000. Geologic Evolution of the Himalayan-Tibetan Orogen. Annual Review of Earth and Planetary Sciences 28:211-280.
Yue P. 2000. Fauna Sinica Osteichthyes: Cypriniformes(III): Beijing: Science Press.
Zan R, Liu W, Song Z. 1985. Tetraploid-hexaploid relationship in Schizothoracinae. Acta. Genet. Sin. 12:137-142 (in Chinese with English abstract).
Zhang K, Sun Y, Ju S, Ma S, Yu J. 2010. The neotectonic process causing the conversion of the Qinghai Lake from an outflow lake into an interior lake. Remote Sensing for Land & Resources 11:77-81.
Zhou C, Xiao S, Liu Y, Mou Z, Zhou J, Pan Y, Zhang C, Wang J, Deng X, Zou M, et al. 2020. Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau. Sci Data 7:28.