{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T11:25:12Z","timestamp":1762169112713,"version":"build-2065373602"},"reference-count":111,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32271691)"],"award-info":[{"award-number":["32271691)"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Lanzhou University\u2019s \u201cDouble First-Class\u201d Guided Project-Team Building Funding-Research Startup Funds"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"DOI":"10.1186\/s12915-025-02431-4","type":"journal-article","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T09:55:09Z","timestamp":1762163709000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic signatures of subterranean lifestyle and ecological adaptation in Myospalax"],"prefix":"10.1186","volume":"23","author":[{"given":"Na","family":"Wan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaqi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muli","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengzhuo","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haolin","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mozhi","family":"Wen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaolong","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaojie","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yijing","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yige","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eviatar","family":"Nevo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kexin","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,11,3]]},"reference":[{"issue":"11","key":"2431_CR1","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1038\/nrg3522","volume":"14","author":"O Savolainen","year":"2013","unstructured":"Savolainen O, Lascoux M, Meril\u00e4 J. Ecological genomics of local adaptation. Nat Rev Genet. 2013;14(11):807\u201320.","journal-title":"Nat Rev Genet"},{"issue":"2","key":"2431_CR2","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/s41559-023-02275-7","volume":"8","author":"X An","year":"2024","unstructured":"An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, et al. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors. Nat Ecol Evol. 2024;8(2):339\u201351.","journal-title":"Nat Ecol Evol"},{"issue":"5","key":"2431_CR3","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/s41559-019-0864-8","volume":"3","author":"K Wang","year":"2019","unstructured":"Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, et al. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol. 2019;3(5):823\u201333.","journal-title":"Nat Ecol Evol"},{"issue":"4","key":"2431_CR4","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/j.cell.2014.03.054","volume":"157","author":"S Liu","year":"2014","unstructured":"Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 2014;157(4):785\u201394.","journal-title":"Cell"},{"issue":"3722","key":"2431_CR5","first-page":"619","volume":"152","author":"P Bentley","year":"1966","unstructured":"Bentley P. Adaptations of amphibia to arid environments: novel physiological mechanisms not seen in fish aid frogs and toads to conserve water and live in deserts. Sci Cult. 1966;152(3722):619\u201323.","journal-title":"Sci Cult"},{"issue":"10","key":"2431_CR6","doi-asserted-by":"publisher","first-page":"2544","DOI":"10.1093\/molbev\/msy161","volume":"35","author":"KTJ Davies","year":"2018","unstructured":"Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. Limited evidence for parallel molecular adaptations associated with the subterranean niche in mammals: a comparative study of three superorders. Mol Biol Evol. 2018;35(10):2544\u201359.","journal-title":"Mol Biol Evol"},{"issue":"19","key":"2431_CR7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2121819119","volume":"119","author":"X Liu","year":"2022","unstructured":"Liu X, Zhang S, Cai Z, Kuang Z, Wan N, Wang Y, et al. Genomic insights into zokors\u2019 phylogeny and speciation in China. Proc Natl Acad Sci U S A. 2022;119(19):e2121819119.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2431_CR8","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1093\/molbev\/msw221","volume":"34","author":"K He","year":"2017","unstructured":"He K, Shinohara A, Helgen KM, Springer MS, Jiang XL, Campbell KL. Talpid mole phylogeny unites shrew moles and illuminates overlooked cryptic species diversity. Mol Biol Evol. 2017;34(1):78\u201387.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2431_CR9","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1038\/s42003-022-03480-z","volume":"5","author":"G Montoya-Sanhueza","year":"2022","unstructured":"Montoya-Sanhueza G, \u0160affa G, \u0160umbera R, Chinsamy A, Jarvis JUM, Bennett NC. Fossorial adaptations in African mole-rats (Bathyergidae) and the unique appendicular phenotype of naked mole-rats. Commun Biol. 2022;5(1):526.","journal-title":"Commun Biol"},{"issue":"2","key":"2431_CR10","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/molbev\/msaa249","volume":"38","author":"M Policarpo","year":"2021","unstructured":"Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, et al. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Mol Biol Evol. 2021;38(2):589\u2013605.","journal-title":"Mol Biol Evol"},{"issue":"6335","key":"2431_CR11","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1126\/science.aab3896","volume":"356","author":"TJ Park","year":"2017","unstructured":"Park TJ, Reznick J, Peterson BL, Blass G, Omerba\u0161i\u0107 D, Bennett NC, et al. Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat. Science. 2017;356(6335):307\u201311.","journal-title":"Science"},{"issue":"10","key":"2431_CR12","doi-asserted-by":"publisher","first-page":"4562","DOI":"10.1093\/molbev\/msab205","volume":"38","author":"H Jiao","year":"2021","unstructured":"Jiao H, Wang Q, Wang B-J, Li K, L\u00f6vy M, Nevo E, et al. Local adaptation of bitter taste and ecological speciation in a wild mammal. Mol Biol Evol. 2021;38(10):4562\u201372.","journal-title":"Mol Biol Evol"},{"issue":"7","key":"2431_CR13","doi-asserted-by":"publisher","first-page":"2587","DOI":"10.1073\/pnas.1222588110","volume":"110","author":"Y Hadid","year":"2013","unstructured":"Hadid Y, Tzur S, Pavl\u00edcek T, \u0160umbera R, \u0160kl\u00edba J, L\u00f6vy M, et al. Possible incipient sympatric ecological speciation in blind mole rats (Spalax). Proc Natl Acad Sci U S A. 2013;110(7):2587\u201392.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2431_CR14","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1146\/annurev.en.20.010175.001401","volume":"20","author":"JL Cloudsley-Thompson","year":"1975","unstructured":"Cloudsley-Thompson JL. Adaptations of arthropoda to arid environments. Annu Rev Entomol. 1975;20:261\u201383.","journal-title":"Annu Rev Entomol"},{"issue":"2","key":"2431_CR15","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1111\/gcb.16379","volume":"29","author":"FL Newell","year":"2023","unstructured":"Newell FL, Ausprey IJ, Robinson SK. Wet and dry extremes reduce arthropod biomass independently of leaf phenology in the wet tropics. Glob Change Biol. 2023;29(2):308\u201323.","journal-title":"Glob Change Biol"},{"key":"2431_CR16","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14159","volume":"8","author":"C Lo Cascio S\u00e6tre","year":"2017","unstructured":"Lo Cascio S\u00e6tre C, Coleiro C, Austad M, Gauci M, S\u00e6tre GP, Voje KL, et al. Rapid adaptive phenotypic change following colonization of a newly restored habitat. Nat Commun. 2017;8:14159.","journal-title":"Nat Commun"},{"issue":"51","key":"2431_CR17","doi-asserted-by":"publisher","first-page":"13501","DOI":"10.1073\/pnas.1712934114","volume":"114","author":"M Sz\u0171cs","year":"2017","unstructured":"Sz\u0171cs M, Vahsen ML, Melbourne BA, Hoover C, Weiss-Lehman C, Hufbauer RA. Rapid adaptive evolution in novel environments acts as an architect of population range expansion. Proc Natl Acad Sci U S A. 2017;114(51):13501\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"2431_CR18","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1038\/s41588-024-01733-7","volume":"56","author":"Z Han","year":"2024","unstructured":"Han Z, Wang Z, Rittschof D, Huang Z, Chen L, Hao H, et al. New genes helped acorn barnacles adapt to a sessile lifestyle. Nat Genet. 2024;56(5):970\u201381.","journal-title":"Nat Genet"},{"issue":"12","key":"2431_CR19","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1038\/nrm2805","volume":"10","author":"PA Romero","year":"2009","unstructured":"Romero PA, Arnold FH. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol. 2009;10(12):866\u201376.","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"5","key":"2431_CR20","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/nrg2958","volume":"12","author":"C Alkan","year":"2011","unstructured":"Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363\u201376.","journal-title":"Nat Rev Genet"},{"issue":"8","key":"2431_CR21","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/j.tig.2023.04.005","volume":"39","author":"JD Galbraith","year":"2023","unstructured":"Galbraith JD, Hayward A. The influence of transposable elements on animal colouration. Trends Genet. 2023;39(8):624\u201338.","journal-title":"Trends Genet"},{"issue":"6","key":"2431_CR22","doi-asserted-by":"publisher","first-page":"2175","DOI":"10.1073\/pnas.1808631116","volume":"116","author":"G Fudenberg","year":"2019","unstructured":"Fudenberg G, Pollard KS. Chromatin features constrain structural variation across evolutionary timescales. Proc Natl Acad Sci U S A. 2019;116(6):2175\u201380.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2431_CR23","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1534\/genetics.117.300572","volume":"208","author":"C Inversions","year":"2018","unstructured":"Inversions C. Local Adaptation and Speciation. Genetics. 2018;208(1):433.","journal-title":"Genetics"},{"issue":"9","key":"2431_CR24","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1073\/pnas.3.9.555","volume":"3","author":"AH Sturtevant","year":"1917","unstructured":"Sturtevant AH. Genetic factors affecting the strength of linkage in Drosophila. Proc Natl Acad Sci U S A. 1917;3(9):555\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"2431_CR25","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/j.cell.2010.10.027","volume":"143","author":"JM Kidd","year":"2010","unstructured":"Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell. 2010;143(5):837\u201347.","journal-title":"Cell"},{"issue":"8","key":"2431_CR26","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/s41588-020-0646-x","volume":"52","author":"D Porubsky","year":"2020","unstructured":"Porubsky D, Sanders AD, H\u00f6ps W, Hsieh P, Sulovari A, Li R, et al. Recurrent inversion toggling and great ape genome evolution. Nat Genet. 2020;52(8):849\u201358.","journal-title":"Nat Genet"},{"issue":"5","key":"2431_CR27","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","volume":"161","author":"DG Lupi\u00e1\u00f1ez","year":"2015","unstructured":"Lupi\u00e1\u00f1ez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161(5):1012\u201325.","journal-title":"Cell"},{"issue":"7","key":"2431_CR28","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1038\/s41588-022-01116-w","volume":"54","author":"S Zhang","year":"2022","unstructured":"Zhang S, Plummer D, Lu L, Cui J, Xu W, Wang M, et al. Deeploop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution. Nat Genet. 2022;54(7):1013\u201325.","journal-title":"Nat Genet"},{"issue":"10","key":"2431_CR29","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/nrg3604","volume":"14","author":"LB Scheinfeldt","year":"2013","unstructured":"Scheinfeldt LB, Tishkoff SA. Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet. 2013;14(10):692\u2013702.","journal-title":"Nat Rev Genet"},{"issue":"331","key":"2431_CR30","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1206\/582-4.1","volume":"2009","author":"LJ Flynn","year":"2009","unstructured":"Flynn LJ. The antiquity of Rhizomys and independent acquisition of fossorial traits in subterranean muroids. B Am Mus Nat Hist. 2009;2009(331):128\u201356.","journal-title":"B Am Mus Nat Hist"},{"issue":"36","key":"2431_CR31","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adt2282","volume":"11","author":"N Wan","year":"2025","unstructured":"Wan N, Duan Q, Cai Z, Zhu Z, Wang J, Tian Y, et al. Aplf\/Dna2 variants drive chromosomal fission and accelerate speciation in zokors. Sci Adv. 2025;11(36):eadt2282.","journal-title":"Sci Adv"},{"key":"2431_CR32","doi-asserted-by":"publisher","DOI":"10.3390\/ani14162334","author":"Z Shang","year":"2024","unstructured":"Shang Z, Chen K, Han T, Bu F, Sun S, Zhu N, et al. Natural foraging selection and gut microecology of two subterranean rodents from the Eurasian Steppe in China. Animals. 2024. https:\/\/doi.org\/10.3390\/ani14162334.","journal-title":"Animals"},{"issue":"11","key":"2431_CR33","doi-asserted-by":"publisher","first-page":"3943","DOI":"10.3390\/ijerph9113943","volume":"9","author":"H Cai","year":"2012","unstructured":"Cai H, Zhang S, Yang X. Forest dynamics and their phenological response to climate warming in the Khingan Mountains, northeastern China. Int J Environ Res Public Health. 2012;9(11):3943\u201353.","journal-title":"Int J Environ Res Public Health"},{"issue":"6","key":"2431_CR34","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1016\/j.cmet.2018.04.003","volume":"27","author":"P Bu","year":"2018","unstructured":"Bu P, Chen KY, Xiang K, Johnson C, Crown SB, Rakhilin N, et al. Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. Cell Metab. 2018;27(6):1249-1262.e1244.","journal-title":"Cell Metab"},{"issue":"11","key":"2431_CR35","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1038\/s41418-024-01395-2","volume":"31","author":"C Frezza","year":"2024","unstructured":"Frezza C. Fructose: the sweet(er) side of the Warburg effect. Cell Death Differ. 2024;31(11):1395\u20137.","journal-title":"Cell Death Differ"},{"issue":"5","key":"2431_CR36","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41588-020-0615-4","volume":"52","author":"A Cortese","year":"2020","unstructured":"Cortese A, Zhu Y, Rebelo AP, Negri S, Courel S, Abreu L, et al. Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes. Nat Genet. 2020;52(5):473\u201381.","journal-title":"Nat Genet"},{"issue":"5","key":"2431_CR37","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.1053\/j.gastro.2020.07.036","volume":"159","author":"JM Ramos Pittol","year":"2020","unstructured":"Ramos Pittol JM, Milona A, Morris I, Willemsen ECL, van der Veen SW, Kalkhoven E, et al. FXR Isoforms Control Different Metabolic Functions in Liver Cells via Binding to Specific DNA Motifs. Gastroenterology. 2020;159(5):1853-1865.e1810.","journal-title":"Gastroenterology"},{"issue":"7057","key":"2431_CR38","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nature03928","volume":"437","author":"IB Lobov","year":"2005","unstructured":"Lobov IB, Rao S, Carroll TJ, Vallance JE, Ito M, Ondr JK, et al. WNT7b mediates macrophage-induced programmed cell death in patterning of the vasculature. Nature. 2005;437(7057):417\u201321.","journal-title":"Nature"},{"issue":"7458","key":"2431_CR39","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1038\/nature12234","volume":"499","author":"X Tian","year":"2013","unstructured":"Tian X, Azpurua J, Hine C, Vaidya A, Myakishev-Rempel M, Ablaeva J, et al. High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat. Nature. 2013;499(7458):346\u20139.","journal-title":"Nature"},{"issue":"7692","key":"2431_CR40","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature25477","volume":"554","author":"ZM Zhang","year":"2018","unstructured":"Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, et al. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature. 2018;554(7692):387\u201391.","journal-title":"Nature"},{"issue":"1","key":"2431_CR41","doi-asserted-by":"publisher","first-page":"27","DOI":"10.15298\/rusjtheriol.13.1.04","volume":"13","author":"AY Puzachenko","year":"2014","unstructured":"Puzachenko AY, Pavlenko MV, Korablev VP, Tsvirka MVJ. Karyotype, genetic and morphological variability in North China zokor, Myospalax psilurus (Rodentia, Spalacidae, Myospalacinae). Russ J Theriol. 2014;13(1):27\u201346.","journal-title":"Russ J Theriol"},{"issue":"10","key":"2431_CR42","doi-asserted-by":"publisher","first-page":"1448","DOI":"10.1101\/gr.6553207","volume":"17","author":"LR Saraiva","year":"2007","unstructured":"Saraiva LR, Korsching SI. A novel olfactory receptor gene family in teleost fish. Genome Res. 2007;17(10):1448\u201357.","journal-title":"Genome Res"},{"key":"2431_CR43","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad069","author":"L Gozashti","year":"2023","unstructured":"Gozashti L, Feschotte C, Hoekstra HE. Transposable element interactions shape the ecology of the deer mouse genome. Mol Biol Evol. 2023. https:\/\/doi.org\/10.1093\/molbev\/msad069.","journal-title":"Mol Biol Evol"},{"key":"2431_CR44","doi-asserted-by":"publisher","first-page":"7604","DOI":"10.1038\/ncomms8604","volume":"6","author":"WA Pastor","year":"2015","unstructured":"Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, et al. Erratum: MORC1 represses transposable elements in the mouse male germline. Nat Commun. 2015;6:7604.","journal-title":"Nat Commun"},{"issue":"3","key":"2431_CR45","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/nrc2344","volume":"8","author":"RG Bristow","year":"2008","unstructured":"Bristow RG, Hill RP. Hypoxia and metabolism. Hypoxia, DNA repair and genetic instability. Nat Rev Cancer. 2008;8(3):180\u201392.","journal-title":"Nat Rev Cancer"},{"key":"2431_CR46","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4347","volume":"5","author":"A \u00c1lvarez-Quil\u00f3n","year":"2014","unstructured":"\u00c1lvarez-Quil\u00f3n A, Serrano-Ben\u00edtez A, Lieberman JA, Quintero C, S\u00e1nchez-Guti\u00e9rrez D, Escudero LM, et al. ATM specifically mediates repair of double-strand breaks with blocked DNA ends. Nat Commun. 2014;5:3347.","journal-title":"Nat Commun"},{"issue":"5547","key":"2431_CR47","doi-asserted-by":"publisher","first-page":"1713","DOI":"10.1126\/science.1065521","volume":"294","author":"D Cortez","year":"2001","unstructured":"Cortez D, Guntuku S, Qin J, Elledge SJ. ATR and ATRIP: partners in checkpoint signaling. Science. 2001;294(5547):1713\u20136.","journal-title":"Science"},{"issue":"5","key":"2431_CR48","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.molcel.2013.07.023","volume":"51","author":"G Lossaint","year":"2013","unstructured":"Lossaint G, Larroque M, Ribeyre C, Bec N, Larroque C, D\u00e9caillet C, et al. FANCD2 binds MCM proteins and controls replisome function upon activation of s phase checkpoint signaling. Mol Cell. 2013;51(5):678\u201390.","journal-title":"Mol Cell"},{"issue":"5","key":"2431_CR49","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1161\/01.CIR.0000154543.07679.08","volume":"111","author":"RD Machado","year":"2005","unstructured":"Machado RD, James V, Southwood M, Harrison RE, Atkinson C, Stewart S, et al. Investigation of second genetic hits at the BMPR2 locus as a modulator of disease progression in familial pulmonary arterial hypertension. Circulation. 2005;111(5):607\u201313.","journal-title":"Circulation"},{"issue":"2","key":"2431_CR50","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1073\/pnas.022630199","volume":"99","author":"JL Arbiser","year":"2002","unstructured":"Arbiser JL, Petros J, Klafter R, Govindajaran B, McLaughlin ER, Brown LF, et al. Reactive oxygen generated by Nox1 triggers the angiogenic switch. Proc Natl Acad Sci USA. 2002;99(2):715\u201320.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"2431_CR51","doi-asserted-by":"publisher","first-page":"7334","DOI":"10.1038\/s41467-021-27562-4","volume":"12","author":"D Hidalgo","year":"2021","unstructured":"Hidalgo D, Bejder J, Pop R, Gellatly K, Hwang Y, Maxwell Scalf S, et al. EpoR stimulates rapid cycling and larger red cells during mouse and human erythropoiesis. Nat Commun. 2021;12(1):7334.","journal-title":"Nat Commun"},{"issue":"36","key":"2431_CR52","doi-asserted-by":"publisher","first-page":"14360","DOI":"10.1073\/pnas.0706777104","volume":"104","author":"O Ravid","year":"2007","unstructured":"Ravid O, Shams I, Ben Califa N, Nevo E, Avivi A, Neumann D. An extracellular region of the erythropoietin receptor of the subterranean blind mole rat Spalax enhances receptor maturation. Proc Natl Acad Sci U S A. 2007;104(36):14360\u20135.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"18","key":"2431_CR53","doi-asserted-by":"publisher","first-page":"11718","DOI":"10.1073\/pnas.182423299","volume":"99","author":"A Avivi","year":"2002","unstructured":"Avivi A, Oster H, Joel A, Beiles A, Albrecht U, Nevo E. Circadian genes in a blind subterranean mammal part II: conservation and uniqueness of the three Period homologs in the blind subterranean mole rat, Spalax ehrenbergi superspecies. Proc Natl Acad Sci U S A. 2002;99(18):11718\u201323.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"2431_CR54","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2025.116110","volume":"44","author":"K Li","year":"2025","unstructured":"Li K, Liu Y, Zhang Y, Fan Z, Hu X, Lai X, et al. Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals. Cell Rep. 2025;44(8):116110.","journal-title":"Cell Rep"},{"key":"2431_CR55","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2021.626240","volume":"12","author":"J Lin","year":"2021","unstructured":"Lin J, Fan L, Han Y, Guo J, Hao Z, Cao L, et al. The mTORC1\/eIF4E\/HIF-1\u03b1 Pathway Mediates Glycolysis to Support Brain Hypoxia Resistance in the Gansu Zokor. Eospalax cansus Front Physiol. 2021;12:626240.","journal-title":"Eospalax cansus Front Physiol"},{"issue":"2","key":"2431_CR56","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/s43587-021-00029-3","volume":"1","author":"M Izraelson","year":"2021","unstructured":"Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, et al. Distinct organization of adaptive immunity in the long-lived rodent Spalax galili. Nat Aging. 2021;1(2):179\u201389.","journal-title":"Nat Aging"},{"issue":"3","key":"2431_CR57","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1111\/1749-4877.12849","volume":"20","author":"K An","year":"2025","unstructured":"An K, Yao B, Tan Y, Kang Y, Wang Z, Su J. Spermatocytes are the terminals of germ cell differentiation in plateau zokor (Eospalax baileyi) during the non-breeding season. Integr Zool. 2025;20(3):608\u201322.","journal-title":"Integr Zool"},{"issue":"22","key":"2431_CR58","doi-asserted-by":"publisher","first-page":"5765","DOI":"10.1111\/mec.16174","volume":"30","author":"T Zhang","year":"2021","unstructured":"Zhang T, Chen J, Zhang J, Guo YT, Zhou X, Li MW, et al. Phenotypic and genomic adaptations to the extremely high elevation in plateau zokor (Myospalax baileyi). Mol Ecol. 2021;30(22):5765\u201379.","journal-title":"Mol Ecol"},{"issue":"5","key":"2431_CR59","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1016\/j.celrep.2014.07.030","volume":"8","author":"X Fang","year":"2014","unstructured":"Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, et al. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Rep. 2014;8(5):1354\u201364.","journal-title":"Cell Rep"},{"issue":"8","key":"2431_CR60","doi-asserted-by":"publisher","first-page":"2272","DOI":"10.1172\/JCI28414","volume":"116","author":"G Jarad","year":"2006","unstructured":"Jarad G, Cunningham J, Shaw AS, Miner JH. Proteinuria precedes podocyte abnormalities inLamb2-\/- mice, implicating the glomerular basement membrane as an albumin barrier. J Clin Invest. 2006;116(8):2272\u20139.","journal-title":"J Clin Invest"},{"issue":"16","key":"2431_CR61","doi-asserted-by":"publisher","first-page":"1875","DOI":"10.1101\/gad.8.16.1875","volume":"8","author":"P Lev\u00e9en","year":"1994","unstructured":"Lev\u00e9en P, Pekny M, Gebre-Medhin S, Swolin B, Larsson E, Betsholtz C. Mice deficient for PDGF B show renal, cardiovascular, and hematological abnormalities. Genes Dev. 1994;8(16):1875\u201387.","journal-title":"Genes Dev"},{"issue":"1","key":"2431_CR62","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.cmet.2006.04.008","volume":"4","author":"K Bouzakri","year":"2006","unstructured":"Bouzakri K, Zachrisson A, Al-Khalili L, Zhang BB, Koistinen HA, Krook A, et al. siRNA-based gene silencing reveals specialized roles of IRS-1\/Akt2 and IRS-2\/Akt1 in glucose and lipid metabolism in human skeletal muscle. Cell Metab. 2006;4(1):89\u201396.","journal-title":"Cell Metab"},{"issue":"12","key":"2431_CR63","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1038\/nm1201-1332","volume":"7","author":"T Grand-Perret","year":"2001","unstructured":"Grand-Perret T, Bouillot A, Perrot A, Commans S, Walker M, Issandou M. SCAP ligands are potent new lipid-lowering drugs. Nat Med. 2001;7(12):1332\u20138.","journal-title":"Nat Med"},{"issue":"9","key":"2431_CR64","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/s41581-023-00734-9","volume":"19","author":"FH Login","year":"2023","unstructured":"Login FH, Nejsum LN. Aquaporin water channels: roles beyond renal water handling. Nat Rev Nephrol. 2023;19(9):604\u201318.","journal-title":"Nat Rev Nephrol"},{"key":"2431_CR65","doi-asserted-by":"publisher","first-page":"3771","DOI":"10.1016\/j.ijbiomac.2020.08.251","volume":"164","author":"P Chen","year":"2020","unstructured":"Chen P, Xiao WF, Pan MH, Xiao JS, Feng YJ, Dong ZQ, et al. Comparative genome-wide DNA methylation analysis reveals epigenomic differences in response to heat-humidity stress in Bombyx mori. Int J Biol Macromol. 2020;164:3771\u20139.","journal-title":"Int J Biol Macromol"},{"issue":"7","key":"2431_CR66","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1111\/mec.15401","volume":"29","author":"A Tigano","year":"2020","unstructured":"Tigano A, Colella JP, MacManes MD. Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent. Mol Ecol. 2020;29(7):1300\u201314.","journal-title":"Mol Ecol"},{"issue":"6604","key":"2431_CR67","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1126\/science.abg0718","volume":"377","author":"ER Hager","year":"2022","unstructured":"Hager ER, Harringmeyer OS, Wooldridge TB, Theingi S, Gable JT, McFadden S, et al. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science. 2022;377(6604):399\u2013405.","journal-title":"Science"},{"issue":"2","key":"2431_CR68","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.cub.2021.11.019","volume":"32","author":"I Sanchez-Donoso","year":"2022","unstructured":"Sanchez-Donoso I, Ravagni S, Rodr\u00edguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, et al. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol. 2022;32(2):462-469.e466.","journal-title":"Curr Biol"},{"doi-asserted-by":"crossref","unstructured":"Jay P, Whibley A, Fr\u00e9zal L, Rodr\u00edguez de Cara M, Nowell RW, Mallet J et al: Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion. Curr Biol. 2018, 28(11):1839\u20131845.e1833.","key":"2431_CR69","DOI":"10.1016\/j.cub.2018.04.072"},{"issue":"1","key":"2431_CR70","doi-asserted-by":"publisher","first-page":"6833","DOI":"10.1038\/s41467-021-27173-z","volume":"12","author":"ER Funk","year":"2021","unstructured":"Funk ER, Mason NA, P\u00e1lsson S, Albrecht T, Johnson JA, Taylor SA. A supergene underlies linked variation in color and morphology in a Holarctic songbird. Nat Commun. 2021;12(1):6833.","journal-title":"Nat Commun"},{"issue":"6744","key":"2431_CR71","doi-asserted-by":"publisher","DOI":"10.1126\/science.adp3745","volume":"388","author":"Z Gompert","year":"2025","unstructured":"Gompert Z, Feder JL, Parchman TL, Planidin NP, Whiting FJH, Nosil P. Adaptation repeatedly uses complex structural genomic variation. Science. 2025;388(6744):eadp3745.","journal-title":"Science"},{"doi-asserted-by":"publisher","unstructured":"Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol. 2022(12). https:\/\/doi.org\/10.1038\/s41559-022-01890-0.","key":"2431_CR72","DOI":"10.1038\/s41559-022-01890-0"},{"issue":"1","key":"2431_CR73","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s41588-019-0561-1","volume":"52","author":"JA Beagan","year":"2020","unstructured":"Beagan JA, Phillips-Cremins JE. On the existence and functionality of topologically associating domains. Nat Genet. 2020;52(1):8\u201316.","journal-title":"Nat Genet"},{"issue":"1","key":"2431_CR74","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/nrg705","volume":"3","author":"RV Samonte","year":"2002","unstructured":"Samonte RV, Eichler EE. Segmental duplications and the evolution of the primate genome. Nat Rev Genet. 2002;3(1):65\u201372.","journal-title":"Nat Rev Genet"},{"key":"2431_CR75","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac101","author":"K Huang","year":"2022","unstructured":"Huang K, Ostevik KL, Elphinstone C, Todesco M, Bercovich N, Owens GL, et al. Mutation load in sunflower inversions is negatively correlated with inversion heterozygosity. Mol Biol Evol. 2022. https:\/\/doi.org\/10.1093\/molbev\/msac101.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2431_CR76","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz159","volume":"9","author":"N Hecker","year":"2020","unstructured":"Hecker N, Hiller M. A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers. Gigascience. 2020;9(1):giz159.","journal-title":"Gigascience"},{"issue":"4","key":"2431_CR77","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004;14(4):708\u201315.","journal-title":"Genome Res"},{"issue":"9","key":"2431_CR78","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"AJ Stamatakis","year":"2014","unstructured":"Stamatakis AJ. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312\u20133.","journal-title":"Bioinformatics"},{"issue":"8","key":"2431_CR79","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z. PAML4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586\u201391.","journal-title":"Mol Biol Evol"},{"issue":"5","key":"2431_CR80","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","volume":"67","author":"A Rambaut","year":"2018","unstructured":"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.","journal-title":"Syst Biol"},{"key":"2431_CR81","first-page":"63","volume":"6","author":"H De Bruijn","year":"2013","unstructured":"De Bruijn H, Markovi\u0107 Z, Wessels W. Late Oligocene rodents from Banovi\u0107i (Bosnia and Herzegovina). Palaeodiversity. 2013;6:63\u2013105.","journal-title":"Palaeodiversity"},{"issue":"4","key":"2431_CR82","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1093\/molbev\/msv037","volume":"32","author":"SB Hedges","year":"2015","unstructured":"Hedges SB, Marin J, Suleski M, Paymer M, Kumar S. Tree of life reveals clock-like speciation and diversification. Mol Biol Evol. 2015;32(4):835\u201345.","journal-title":"Mol Biol Evol"},{"issue":"9","key":"2431_CR83","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0162624","volume":"11","author":"JJ Astrin","year":"2016","unstructured":"Astrin JJ, H\u00f6fer H, Spelda J, Holstein J, Bayer S, Hendrich L, et al. Towards a DNA barcode reference database for spiders and harvestmen of Germany. PLoS ONE. 2016;11(9):e0162624.","journal-title":"PLoS ONE"},{"issue":"1","key":"2431_CR84","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/bib\/bbq072","volume":"12","author":"MJ Hubisz","year":"2011","unstructured":"Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space\/time models. Brief Bioinform. 2011;12(1):41\u201351.","journal-title":"Brief Bioinform"},{"issue":"8","key":"2431_CR85","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034\u201350.","journal-title":"Genome Res"},{"issue":"14","key":"2431_CR86","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"16","key":"2431_CR87","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25(16):2078\u20139.","journal-title":"Bioinformatics"},{"issue":"9","key":"2431_CR88","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297\u2013303.","journal-title":"Genome Res"},{"issue":"2","key":"2431_CR89","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/bioinformatics\/btq635","volume":"27","author":"V Boeva","year":"2011","unstructured":"Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, et al. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics. 2011;27(2):268\u20139.","journal-title":"Bioinformatics"},{"issue":"15","key":"2431_CR90","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156\u20138.","journal-title":"Bioinformatics"},{"issue":"10","key":"2431_CR91","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1093\/bioinformatics\/bty875","volume":"35","author":"C Zhang","year":"2019","unstructured":"Zhang C, Dong SS, Xu JY, He WM, Yang TL. Poplddecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019;35(10):1786\u20138.","journal-title":"Bioinformatics"},{"issue":"suppl_1","key":"2431_CR92","doi-asserted-by":"publisher","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","volume":"21","author":"AL Price","year":"2005","unstructured":"Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(suppl_1):i351\u20138.","journal-title":"Bioinformatics"},{"key":"2431_CR93","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae068","author":"T Baril","year":"2024","unstructured":"Baril T, Galbraith J, Hayward A. Earl grey: a fully automated user-friendly transposable element annotation and analysis pipeline. Mol Biol Evol. 2024. https:\/\/doi.org\/10.1093\/molbev\/msae068.","journal-title":"Mol Biol Evol"},{"issue":"15","key":"2431_CR94","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114\u201320.","journal-title":"Bioinformatics"},{"issue":"8","key":"2431_CR95","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907\u201315.","journal-title":"Nat Biotechnol"},{"issue":"22","key":"2431_CR96","doi-asserted-by":"publisher","first-page":"3593","DOI":"10.1093\/bioinformatics\/btv422","volume":"31","author":"Y Jin","year":"2015","unstructured":"Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"2431_CR97","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13100-021-00259-7","volume":"13","author":"C Goubert","year":"2022","unstructured":"Goubert C, Craig RJ, Bilat AF, Peona V, Vogan AA, Protasio AV. A beginner\u2019s guide to manual curation of transposable elements. Mob DNA. 2022;13(1):7.","journal-title":"Mob DNA"},{"issue":"3","key":"2431_CR98","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.191","volume":"3","author":"W Shen","year":"2024","unstructured":"Shen W, Sipos B, Zhao L. SeqKit2: a swiss army knife for sequence and alignment processing. iMeta. 2024;3(3):e191.","journal-title":"iMeta"},{"issue":"6643","key":"2431_CR99","doi-asserted-by":"publisher","DOI":"10.1126\/science.abn3107","volume":"380","author":"BM Kirilenko","year":"2023","unstructured":"Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, et al. Integrating gene annotation with orthology inference at scale. Science. 2023;380(6643):eabn3107.","journal-title":"Science"},{"issue":"1","key":"2431_CR100","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1186\/s12859-017-1909-0","volume":"18","author":"JM Gaspar","year":"2017","unstructured":"Gaspar JM, Hart RP. Dmrfinder: efficiently identifying differentially methylated regions from MethylC-seq data. BMC Bioinformatics. 2017;18(1):528.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"2431_CR101","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996\u20131006.","journal-title":"Genome Res"},{"issue":"6","key":"2431_CR102","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDtools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841\u20132.","journal-title":"Bioinformatics"},{"issue":"1","key":"2431_CR103","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1911-0","volume":"20","author":"M Goel","year":"2019","unstructured":"Goel M, Sun H, Jiao W-B, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019;20(1):1\u201313.","journal-title":"Genome Biol"},{"issue":"1","key":"2431_CR104","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944","volume":"14","author":"G Mar\u00e7ais","year":"2018","unstructured":"Mar\u00e7ais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14(1):e1005944.","journal-title":"PLoS Comput Biol"},{"issue":"14","key":"2431_CR105","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","volume":"32","author":"HJ Li","year":"2016","unstructured":"Li HJ. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32(14):2103\u201310.","journal-title":"Bioinformatics"},{"issue":"11","key":"2431_CR106","doi-asserted-by":"publisher","first-page":"4867","DOI":"10.1093\/molbev\/msab212","volume":"38","author":"A Li","year":"2021","unstructured":"Li A, Wang J, Sun K, Wang S, Zhao X, Wang T, et al. Two reference-quality sea snake genomes reveal their divergent evolution of adaptive traits and venom systems. Mol Biol Evol. 2021;38(11):4867\u201383.","journal-title":"Mol Biol Evol"},{"issue":"17","key":"2431_CR107","doi-asserted-by":"publisher","first-page":"i706","DOI":"10.1093\/bioinformatics\/bty586","volume":"34","author":"I Numanagi\u0107","year":"2018","unstructured":"Numanagi\u0107 I, G\u00f6kkaya AS, Zhang L, Berger B, Alkan C, Hach FJ. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018;34(17):i706\u201314.","journal-title":"Bioinformatics"},{"issue":"2","key":"2431_CR108","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80\u201392.","journal-title":"Fly"},{"issue":"1","key":"2431_CR109","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-015-0831-x","volume":"16","author":"N Servant","year":"2015","unstructured":"Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C-J, Vert J-P, et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015;16(1):1\u201311.","journal-title":"Genome Biol"},{"doi-asserted-by":"crossref","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357\u20139.","key":"2431_CR110","DOI":"10.1038\/nmeth.1923"},{"issue":"7559","key":"2431_CR111","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1038\/nature14450","volume":"523","author":"E Crane","year":"2015","unstructured":"Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature. 2015;523(7559):240\u20134.","journal-title":"Nature"}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02431-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-025-02431-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02431-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T11:07:47Z","timestamp":1762168067000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-025-02431-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,3]]},"references-count":111,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["2431"],"URL":"https:\/\/doi.org\/10.1186\/s12915-025-02431-4","relation":{},"ISSN":["1741-7007"],"issn-type":[{"type":"electronic","value":"1741-7007"}],"subject":[],"published":{"date-parts":[[2025,11,3]]},"assertion":[{"value":"4 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All procedures applied in\n                      M. aspalax\n                      and\n                      M. psilurus\n                      sample collection were reviewed and approved by the\u00a0Institutional Ethics Committee of the College of Ecology, Lanzhou University (Approval No.: EAF2020003).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"332"}}