{"id":86664,"date":"2025-09-26T11:55:18","date_gmt":"2025-09-26T11:55:18","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/86664\/"},"modified":"2025-09-26T11:55:18","modified_gmt":"2025-09-26T11:55:18","slug":"chromosome-level-genome-assembly-for-sichuan-taimen-hucho-bleekeri-reveals-the-extraordinary-tandem-repeat-proportions-and-its-persistent-population-shrinkage-bmc-genomics","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/86664\/","title":{"rendered":"Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage | BMC Genomics"},"content":{"rendered":"
  • \n

    Wang K, Zhang SH, Wang DQ, Wu JM, Wang CY, Wei QW. Conservation genetics assessment and phylogenetic relationships of critically endangered Hucho bleekeri in China. J Appl Ichthyol. 2016;32(2):343\u20139.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hu M, Wang Y, Cao L, Xiong B. Threatened fishes of the world: Hucho bleekeri kimura, 1934 (Salmonidae). Environ Biol Fishes. 2008;82:385\u20136.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Allendorf FW, Hard JJ. Human-induced evolution caused by unnatural selection through harvest of wild animals. Proc Natl Acad Sci USA. 2009;106(Suppl 1):9987\u201394.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sadovy de Mitcheson Y, Craig MT, Bertoncini AA, Carpenter KE, Cheung WW, Choat JH, Cornish AS, Fennessy ST, Ferreira BP, Heemstra PCJF. Fishing groupers towards extinction: a global assessment of threats and extinction risks in a billion dollar fishery. Fish Fish. 2013;14(2):119\u201336.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sung W, Peiqi Y, Yiyu C, Commission ESS. China red data book of endangered animals: pisces. Beijing: Science; 1998.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Song Z. Hucho bleekeri. The IUCN Red List of Threatened Species. Version 2014.3. 2012.<\/p>\n<\/li>\n

  • \n

    Allendorf FW, Hohenlohe PA, Luikart G. Genomics and the future of conservation genetics. Nat Rev Genet. 2010;11(10):697\u2013709.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kohn MH, Murphy WJ, Ostrander EA, Wayne RK. Genomics and conservation genetics. Trends Ecol Evol. 2006;21(11):629\u201337.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xue DX, Xing TF, Liu JX. A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation. Mol Ecol Resour. 2022;22(5):1892\u2013905.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu X, Zeng H, Wang C, Bo J, Gan X, Fang C, et al. Improved genome assembly of Chinese sucker (Myxocyprinus asiaticus) provides insights into the identification and characterization of pharyngeal teeth related maker genes in cyprinoidei. Water Biology and Security. 2022;1(3):100049.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhu W, Wang Z, Li H, Li P, Ni L, Jiao L, et al. A chromosome-level genome of Brachymystax tsinlingensis provides resources and insights into salmonids evolution. G3 Genes|Genomes|Genetics. 2022;12(8):jkac162.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brandies P, Peel E, Hogg CJ, Belov K. The value of reference genomes in the conservation of threatened species. Genes (Basel). 2019;10(11):846.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Waples RS, Naish KA, Primmer CR. Conservation and management of salmon in the age of genomics. Annu Rev Anim Biosci. 2020;8:117\u201343.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen Y, Yang H, Gong Q, Chen Y, Tu Q, Li H. Isolation and characterization of 34 SNP markers in Hucho bleekeri. Conserv Genet Resour. 2020;12:157\u201360.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhang Y, Luan P, Ren G, Hu G, Yin J. Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan Taimen (Hucho bleekeri) using genome-wide SNP markers. Ecol Evol. 2020;10(3):1390\u2013400.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen Y, Yang H, Chen Y, Song M, Liu B, Song J, et al. Full-length transcriptome sequencing and identification of immune-related genes in the critically endangered Hucho bleekeri. Dev Comp Immunol. 2021;116:103934.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae genome: features, evolutionary and phylogenetic characteristics. Genes. 2022;13(12):2221.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 2017;18(1):111.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019;37(10):1155\u201362.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome. 2016;59(5):295\u2013310.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Horreo JL. Revisiting the mitogenomic phylogeny of salmoninae: new insights thanks to recent sequencing advances. PeerJ. 2017;5:e3828.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lecaudey LA, Schliewen UK, Osinov AG, Taylor EB, Bernatchez L, Weiss SJ. Inferring phylogenetic structure, hybridization and divergence times within salmoninae (Teleostei: Salmonidae) using RAD-sequencing. Mol Phylogenet Evol. 2018;124:82\u201399.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Galland LM, Simmons JB, Jahner JP, Luzuriaga-Neira AR, Sloat MR, Chandra S, et al. Hierarchical genetic structure and implications for conservation of the world\u2019s largest salmonid, Hucho taimen. Sci Rep. 2021;11(1):20508.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kaus A, Michalski S, H\u00e4nfling B, Karthe D, Borchardt D, Durka W. Fish conservation in the land of steppe and sky: evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins. Ecol Evol. 2019;9(6):3416\u201333.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kucinski M, Fopp-Bayat D. Phylogenetic analysis of Brachymystax and Hucho genera\u2014summary on evolutionary status within the salmoninae subfamily. J Appl Ichthyol. 2022;38(4):403\u201311.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hilgers L, Liu S, Jensen A, Brown T, Cousins T, Schweiger R, et al. Avoidable false PSMC population size peaks occur across numerous studies. Curr Biol. 2025;35(4):927-e930923.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533(7602):200\u20135.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gundappa MK, To T-H, Gr\u00f8nvold L, Martin SAM, Lien S, Geist J, et al. Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution. Mol Biol Evol. 2022;39(1):msab310.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Smith SR, Normandeau E, Djambazian H, Nawarathna PM, Berube P, Muir AM, et al. A chromosome-anchored genome assembly for lake trout (Salvelinus namaycush). Mol Ecol Resour. 2022;22(2):679\u201394.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    T\u00f8rresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, et al. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics. 2017;18(1):95.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2011;13(1):36\u201346.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Logsdon GA, Vollger MR, Eichler EE. Long-read human genome sequencing and its applications. Nat Rev Genet. 2020;21(10):597\u2013614.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G, et al. Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore. Gigascience. 2020;9(12):giaa123.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Simon M, Hancock JM. Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol. 2009;10(6):R59.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gemayel R, Vinces MD, Legendre M, Verstrepen KJ. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet. 2010;44(1):445\u201377.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li M, Sun C, Xu N, Bian P, Tian X, Wang X, et al. De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on microchromosomes and subtelomeric regions. Mol Biol Evol. 2022;39(4):msac066.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Coggins LW, O\u2019Prey M. DNA tertiary structures formed in vitro by misaligned hybridization of multiple tandem repeat sequences. Nucleic Acids Res. 1989;17(18):7417\u201326.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fan H, Chu JY. A brief review of short tandem repeat mutation. Genomics Proteomics Bioinf. 2007;5(1):7\u201314.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ahmed M, Liang P. Transposable elements are a significant contributor to tandem repeats in the human genome. Int J Genomics. 2012;2012(1):947089.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marteijn JA, Lans H, Vermeulen W, Hoeijmakers JH. Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol. 2014;15(7):465\u201381.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Selby CP, Lindsey-Boltz LA, Li W, Sancar A. Molecular mechanisms of Transcription-Coupled repair. Annu Rev Biochem. 2023;92:115\u201344.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rodriguez F, Arkhipova IR. Transposable elements and polyploid evolution in animals. Curr Opin Genet Dev. 2018;49:115\u201323.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, et al. Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes. Proc Biol Sci. 2018;285(1872):20172732.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Campbell MA, Buser TJ, Alfaro ME, L\u00f3pez JA. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ. 2020;8:e9389.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cr\u00eate-Lafreni\u00e8re A, Weir LK, Bernatchez L. Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling. PLoS One. 2012;7(10):e46662.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    McKay SJ, Trautner J, Smith MJ, Koop BF, Devlin RH. Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. Genome. 2004;47(4):714\u201323.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang Y, Guo R, Li H, Zhang X, Du J, Song Z. The complete mitochondrial genome of the Sichuan Taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae. Mar Genomics. 2011;4(3):221\u20138.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang Y, Xiong F, Song Z. Molecular phylogeny and adaptive mitochondrial DNA evolution of salmonids (Pisces: Salmonidae). Front Genet. 2022;13:903240.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Macqueen DJ, Johnston IA. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc Biol Sci. 2014;281(1778):20132881.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Campbell MA, L\u00f3pez JA, Sado T, Miya M. Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes\u2009+\u2009Salmoniformes based on whole mitochondrial genome sequences. Gene. 2013;530(1):57\u201365.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shedko SV, Miroshnichenko IL, Nemkova GA. Phylogeny of salmonids (Salmoniformes, Salmonidae) and molecular dating: analysis of mtDNA data. Genetika. 2013;49(6):718\u201334.<\/p>\n

    CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Crespi BJ, Fulton MJ. Molecular systematics of salmonidae: combined nuclear data yields a robust phylogeny. Mol Phylogenet Evol. 2004;31(2):658\u201379.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    B\u00f6hme MJP, Palaeoclimatology. Palaeoecology: the miocene Climatic optimum: evidence from ectothermic vertebrates of central Europe. Palaeogeogr Palaeoclimatol Palaeoecol. 2003;195(3\u20134):389\u2013401.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sun J, Zhang Z. Palynological evidence for the mid-Miocene climatic optimum recorded in cenozoic sediments of the Tian Shan range, Northwestern China. Glob Planet Change. 2008;64(1):53\u201368.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shen Z, Tang W, Li K. The analysis of population dynamics of Hucho bleekeri in Markehe river, Qinghai Province. Reserv Fisheries. 2006;26:71\u20133.<\/p>\n

    CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stefanova P, Taseva M, Georgieva T, Gotcheva V, Angelov A. A modified CTAB method for DNA extraction from soybean and meat products. Biotechnol Biotechnol Equip. 2013;27(3):3803\u201310.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res. 2018;46(5):2159\u201368.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-90.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu B, Shi Y, Yuan J, Hu X, Zhang H, Li N, Li Z, Chen Y, Mu D, Fan W. Estimation of genomic characteristics by analyzing k-mer frequency in de Novo genome projects. arXiv. 2013;arXiv:13082012.<\/p>\n<\/li>\n

  • \n

    Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020;11(1):1432.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170\u20135.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3(1):95\u20138.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356(6333):92\u20135.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 2016;3(1):99\u2013101.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roach MJ, Schmidt SA, Borneman AR. Purge haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinf. 2018;19(1):460.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xu M, Guo L, Gu S, Wang O, Zhang R, Peters BA, et al. TGS-gapcloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience. 2020;9(9):giaa094.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sim\u00e3o FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210\u20132.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. Repeatmodeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020;117(17):9451\u20137.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xu Z, Wang H. Ltr_finder: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35(2):W265-8.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ou S, Jiang N. Ltr_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. 2018;176(2):1410\u201322.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ye J, McGinnis S, Madden TL. BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006;34(Web Server issue):W6-9.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tarailo-Graovac M, Chen N. Using repeatmasker to identify repetitive elements in genomic sequences. Curr Protoc. 2009;4:1\u20134.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573\u201380.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32(5):767\u20139.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoff KJ, Lomsadze A, Borodovsky M, Stanke M. Whole-genome annotation with BRAKER. Methods Mol Biol. 2019;1962:65\u201395.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15\u201321.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet. 2016;48(4):427\u201337.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gao G, Magadan S, Waldbieser GC, Youngblood RC, Wheeler PA, Scheffler BE, et al. A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout. G3 Genes|Genomes|Genetics. 2021;11(4):jkab052.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gabriel L, Hoff KJ, Br\u016fna T, Borodovsky M, Stanke M. TSEBRA: transcript selector for BRAKER. BMC Bioinf. 2021;22(1):566.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525\u20137.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Christensen KA, Rondeau EB, Minkley DR, Sakhrani D, Biagi CA, Flores AM, et al. The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One. 2020;15(10):e0240935.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hansen T, Fjelldal PG, Lien S, Smith M, Corton C, Oliver K, et al. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome Open Res. 2021;6:108.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Emms DM, Kelly S. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:1\u201314.<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792\u20137.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312\u20133.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mendes FK, Vanderpool D, Fulton B, Hahn MW. Cafe 5 models variation in evolutionary rates among gene families. Bioinformatics. 2020;36(22\u201323):5516\u20138.<\/p>\n

    CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586\u201391.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kumar S, Suleski M, Craig JM, Kasprowicz AE, Sanderford M, Li M, et al. TimeTree 5: an expanded resource for species divergence times. Mol Biol Evol. 2022. https:\/\/doi.org\/10.1093\/molbev\/msac174<\/a>.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34(suppl2):W609-12.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268\u201374.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 2014;15(1):356.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics. 2021;37(12):1639\u201343.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bouckaert R, Vaughan TG, Barido-Sottani J, Duch\u00eane S, Fourment M, Gavryushkina A, Heled J, Jones G, K\u00fchnert D, De Maio N, et al. BEAST 2.5: an advanced software platform for bayesian evolutionary analysis. PLoS Comput Biol. 2019;15(4):e1006650.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Darriba D, Taboada GL, Doallo R, Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9(8):772\u2013772.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in bayesian phylogenetics using tracer 1.7. Syst Biol. 2018;67(5):901\u20134.<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li H, Durbin R: Inference of human population history from individual whole-genome sequences. Nature 2011, 475(7357):493-496.<\/p>\n<\/li>\n

  • \n

    Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM et al: Twelve years of SAMtools and BCFtools. GigaScience 2021, 10(2):giab008.<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Wang K, Zhang SH, Wang DQ, Wu JM, Wang CY, Wei QW. Conservation genetics assessment and phylogenetic relationships…\n","protected":false},"author":2,"featured_media":86665,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[77],"tags":[2569,18,910,57094,19,17,3544,9693,6720,57093,6719,3549,57096,133,57095],"class_list":{"0":"post-86664","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-animal-genetics-and-genomics","9":"tag-eire","10":"tag-general","11":"tag-genome-assembly","12":"tag-ie","13":"tag-ireland","14":"tag-life-sciences","15":"tag-microarrays","16":"tag-microbial-genetics-and-genomics","17":"tag-n-hucho-bleekerin","18":"tag-plant-genetics-and-genomics","19":"tag-proteomics","20":"tag-salmonid","21":"tag-science","22":"tag-tandem-repeats"},"share_on_mastodon":{"url":"","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/86664","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=86664"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/86664\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/86665"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=86664"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=86664"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=86664"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}