{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T03:30:42Z","timestamp":1791343842392,"version":"4.3.1"},"reference-count":108,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB13020400"],"award-info":[{"award-number":["XDB13020400"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871277"],"award-info":[{"award-number":["31871277"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Yunling Scholar Project, Ten-Thousand Talents Plan of Yunnan Province"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Naked mole-rats (\n                      <jats:italic>Heterocephalus glaber<\/jats:italic>\n                      , NMRs) and blind mole-rats (\n                      <jats:italic>Spalax galili<\/jats:italic>\n                      , BMRs) are representative subterranean rodents that have evolved many extraordinary traits, including hypoxia tolerance, longevity, and cancer resistance. Although multiple candidate loci responsible for these traits have been uncovered by genomic studies, many of them are limited to functional changes to amino acid sequence and little is known about the contributions of other genetic events. To address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, aiming to elucidate the potential roles of pseudogenes in their adaptation to subterranean lifestyle.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We obtained the pseudogene repertoires in NMRs and BMRs, as well as their respective aboveground relatives, guinea pigs and rats, on a genome-wide scale. As a result, 167, 139, 341, and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs, and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. Notably, the pseudogenes in these EFGs might be associated with either regressive (e.g., visual system) or adaptive (e.g., altered DNA damage response) traits. In addition, several pseudogenes including\n                      <jats:italic>TNNI3K<\/jats:italic>\n                      and\n                      <jats:italic>PDE5A<\/jats:italic>\n                      might be associated with specific cardiac features observed in subterranean lineages. Interestingly, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of\n                      <jats:italic>TRIM17<\/jats:italic>\n                      in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating\n                      <jats:italic>TRIM17<\/jats:italic>\n                      function in hypoxia adaptation. Our results also suggested that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12915-022-01243-0","type":"journal-article","created":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T21:02:23Z","timestamp":1645045343000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat"],"prefix":"10.1186","volume":"20","author":[{"given":"Zhizhong","family":"Zheng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Hua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoqiang","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1128-2712","authenticated-orcid":false,"given":"Hui","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,2,17]]},"reference":[{"issue":"1","key":"1243_CR1","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1146\/annurev.es.10.110179.001413","volume":"10","author":"E Nevo","year":"1979","unstructured":"Nevo E. Adaptive convergence and divergence of subterranean mammals. Annu Rev Ecol Syst. 1979;10(1):269\u2013308.","journal-title":"Annu Rev Ecol Syst"},{"issue":"9","key":"1243_CR2","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1073\/pnas.0809620106","volume":"106","author":"VI Perez","year":"2009","unstructured":"Perez VI, Buffenstein R, Masamsetti V, Leonard S, Salmon AB, Mele J, et al. Protein stability and resistance to oxidative stress are determinants of longevity in the longest-living rodent, the naked mole-rat. Proc Natl Acad Sci U S A. 2009;106(9):3059\u201364.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"46","key":"1243_CR3","doi-asserted-by":"publisher","first-page":"19352","DOI":"10.1073\/pnas.0905252106","volume":"106","author":"A Seluanov","year":"2009","unstructured":"Seluanov A, Hine C, Azpurua J, Feigenson M, Bozzella M, Mao Z, et al. Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proc Natl Acad Sci U S A. 2009;106(46):19352\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7372","key":"1243_CR4","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/nature10533","volume":"479","author":"EB Kim","year":"2011","unstructured":"Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011;479(7372):223\u20137.","journal-title":"Nature"},{"issue":"6062","key":"1243_CR5","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1126\/science.1213760","volume":"334","author":"ES Smith","year":"2011","unstructured":"Smith ES, Omerbasic D, Lechner SG, Anirudhan G, Lapatsina L, Lewin GR. The molecular basis of acid insensitivity in the African naked mole-rat. Science. 2011;334(6062):1557\u201360.","journal-title":"Science"},{"issue":"7458","key":"1243_CR6","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":"6335","key":"1243_CR7","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, Omerbasic 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":"8","key":"1243_CR8","doi-asserted-by":"publisher","first-page":"1801","DOI":"10.1073\/pnas.1721160115","volume":"115","author":"Y Zhao","year":"2018","unstructured":"Zhao Y, Tyshkovskiy A, Munoz-Espin D, Tian X, Serrano M, de Magalhaes JP, et al. Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence. Proc Natl Acad Sci U S A. 2018;115(8):1801\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"24","key":"1243_CR9","doi-asserted-by":"publisher","first-page":"13751","DOI":"10.1073\/pnas.181484498","volume":"98","author":"A Avivi","year":"2001","unstructured":"Avivi A, Albrecht U, Oster H, Joel A, Beiles A, Nevo E. Biological clock in total darkness: the Clock\/MOP3 circadian system of the blind subterranean mole rat. Proc Natl Acad Sci U S A. 2001;98(24):13751\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"33","key":"1243_CR10","doi-asserted-by":"publisher","first-page":"12236","DOI":"10.1073\/pnas.0404998101","volume":"101","author":"O Ashur-Fabian","year":"2004","unstructured":"Ashur-Fabian O, Avivi A, Trakhtenbrot L, Adamsky K, Cohen M, Kajakaro G, et al. Evolution of p53 in hypoxia-stressed Spalax mimics human tumor mutation. Proc Natl Acad Sci U S A. 2004;101(33):12236\u201341.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"26","key":"1243_CR11","doi-asserted-by":"publisher","first-page":"9698","DOI":"10.1073\/pnas.0403540101","volume":"101","author":"I Shams","year":"2004","unstructured":"Shams I, Avivi A, Nevo E. Hypoxic stress tolerance of the blind subterranean mole rat: expression of erythropoietin and hypoxia-inducible factor 1 alpha. Proc Natl Acad Sci U S A. 2004;101(26):9698\u2013703.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"42","key":"1243_CR12","doi-asserted-by":"publisher","first-page":"15161","DOI":"10.1073\/pnas.0507279102","volume":"102","author":"NJ Nasser","year":"2005","unstructured":"Nasser NJ, Nevo E, Shafat I, Ilan N, Vlodavsky I, Avivi A. Adaptive evolution of heparanase in hypoxia-tolerant Spalax: gene cloning and identification of a unique splice variant. Proc Natl Acad Sci U S A. 2005;102(42):15161\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"50","key":"1243_CR13","doi-asserted-by":"publisher","first-page":"21570","DOI":"10.1073\/pnas.1015379107","volume":"107","author":"A Avivi","year":"2010","unstructured":"Avivi A, Gerlach F, Joel A, Reuss S, Burmester T, Nevo E, et al. Neuroglobin, cytoglobin, and myoglobin contribute to hypoxia adaptation of the subterranean mole rat Spalax. Proc Natl Acad Sci U S A. 2010;107(50):21570\u20135.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"47","key":"1243_CR14","doi-asserted-by":"publisher","first-page":"19392","DOI":"10.1073\/pnas.1217211109","volume":"109","author":"V Gorbunova","year":"2012","unstructured":"Gorbunova V, Hine C, Tian X, Ablaeva J, Gudkov AV, Nevo E, et al. Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism. Proc Natl Acad Sci U S A. 2012;109(47):19392\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1243_CR15","doi-asserted-by":"publisher","first-page":"3966","DOI":"10.1038\/ncomms4966","volume":"5","author":"X Fang","year":"2014","unstructured":"Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun. 2014;5:3966.","journal-title":"Nat Commun"},{"issue":"3","key":"1243_CR16","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1177\/0300985816630796","volume":"53","author":"MA Delaney","year":"2016","unstructured":"Delaney MA, Ward JM, Walsh TF, Chinnadurai SK, Kerns K, Kinsel MJ, et al. Initial case reports of cancer in naked mole-rats (Heterocephalus glaber). Vet Pathol. 2016;53(3):691\u20136.","journal-title":"Vet Pathol"},{"issue":"4494","key":"1243_CR17","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1126\/science.7209555","volume":"212","author":"JU Jarvis","year":"1981","unstructured":"Jarvis JU. Eusociality in a mammal: cooperative breeding in naked mole-rat colonies. Science. 1981;212(4494):571\u20133.","journal-title":"Science"},{"issue":"1","key":"1243_CR18","doi-asserted-by":"publisher","first-page":"R149","DOI":"10.1152\/ajpregu.2001.280.1.R149","volume":"280","author":"R Buffenstein","year":"2001","unstructured":"Buffenstein R, Woodley R, Thomadakis C, Daly TJ, Gray DA. Cold-induced changes in thyroid function in a poikilothermic mammal, the naked mole-rat. Am J Physiol Regul Integr Comp Physiol. 2001;280(1):R149\u201355.","journal-title":"Am J Physiol Regul Integr Comp Physiol"},{"issue":"6","key":"1243_CR19","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1007\/BF01131581","volume":"81","author":"J Davis-Walton","year":"1994","unstructured":"Davis-Walton J, Sherman PW. Sleep arrhythmia in the eusocial naked mole-rat. Naturwissenschaften. 1994;81(6):272\u20135.","journal-title":"Naturwissenschaften"},{"issue":"1","key":"1243_CR20","first-page":"47","volume":"38","author":"MD Mann","year":"1997","unstructured":"Mann MD, Rehkamper G, Reinke H, Frahm HD, Necker R, Nevo E. Size of somatosensory cortex and of somatosensory thalamic nuclei of the naturally blind mole rat, Spalax ehrenbergi. J Hirnforsch. 1997;38(1):47\u201359.","journal-title":"J Hirnforsch"},{"issue":"Pt 4","key":"1243_CR21","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1242\/jeb.204.4.751","volume":"204","author":"T Kimchi","year":"2001","unstructured":"Kimchi T, Terkel J. Magnetic compass orientation in the blind mole rat Spalax ehrenbergi. J Exp Biol. 2001;204(Pt 4):751\u20138.","journal-title":"J Exp Biol"},{"issue":"5","key":"1243_CR22","doi-asserted-by":"publisher","first-page":"2062","DOI":"10.1073\/pnas.94.5.2062","volume":"94","author":"HR Widmer","year":"1997","unstructured":"Widmer HR, Hoppeler H, Nevo E, Taylor CR, Weibel ER. Working underground: respiratory adaptations in the blind mole rat. Proc Natl Acad Sci U S A. 1997;94(5):2062\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1243_CR23","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1186\/s12862-015-0564-1","volume":"15","author":"K Du","year":"2015","unstructured":"Du K, Yang L, He S. Phylogenomic analyses reveal a molecular signature linked to subterranean adaptation in rodents. BMC Evol Biol. 2015;15:287.","journal-title":"BMC Evol Biol"},{"key":"1243_CR24","doi-asserted-by":"publisher","first-page":"17262","DOI":"10.1038\/srep17262","volume":"5","author":"Y Shao","year":"2015","unstructured":"Shao Y, Li JX, Ge RL, Zhong L, Irwin DM, Murphy RW, et al. Genetic adaptations of the plateau zokor in high-elevation burrows. Sci Rep. 2015;5:17262.","journal-title":"Sci Rep"},{"issue":"10","key":"1243_CR25","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":"1776","key":"1243_CR26","first-page":"20132950","volume":"281","author":"Z Liu","year":"2014","unstructured":"Liu Z, Wang W, Zhang TZ, Li GH, He K, Huang JF, et al. Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals. Proc Biol Sci. 2014;281(1776):20132950.","journal-title":"Proc Biol Sci"},{"issue":"8","key":"1243_CR27","doi-asserted-by":"publisher","first-page":"e21227","DOI":"10.1371\/journal.pone.0021227","volume":"6","author":"A Malik","year":"2011","unstructured":"Malik A, Korol A, Hubner S, Hernandez AG, Thimmapuram J, Ali S, et al. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns. Plos One. 2011;6(8):e21227.","journal-title":"Plos One"},{"key":"1243_CR28","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1186\/1471-2164-13-615","volume":"13","author":"A Malik","year":"2012","unstructured":"Malik A, Korol A, Weber M, Hankeln T, Avivi A, Band M. Transcriptome analysis of the spalax hypoxia survival response includes suppression of apoptosis and tight control of angiogenesis. BMC Genomics. 2012;13:615.","journal-title":"BMC Genomics"},{"issue":"5","key":"1243_CR29","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":"7","key":"1243_CR30","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrg.2016.39","volume":"17","author":"R Albalat","year":"2016","unstructured":"Albalat R, Canestro C. Evolution by gene loss. Nat Rev Genet. 2016;17(7):379\u201391.","journal-title":"Nat Rev Genet"},{"issue":"1","key":"1243_CR31","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nrg3095","volume":"13","author":"PJ Wittkopp","year":"2012","unstructured":"Wittkopp PJ, Kalay G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet. 2012;13(1):59\u201369.","journal-title":"Nat Rev Genet"},{"key":"1243_CR32","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1146\/annurev.ecolsys.39.110707.173441","volume":"40","author":"R Bonduriansky","year":"2009","unstructured":"Bonduriansky R, Day T. Nongenetic inheritance and its evolutionary implications. Annu Rev Ecol Evol Syst. 2009;40:103\u201325.","journal-title":"Annu Rev Ecol Evol Syst"},{"issue":"1","key":"1243_CR33","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1038\/s41467-018-03667-1","volume":"9","author":"V Sharma","year":"2018","unstructured":"Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun. 2018;9(1):1215.","journal-title":"Nat Commun"},{"issue":"9","key":"1243_CR34","doi-asserted-by":"publisher","first-page":"eaaw6671","DOI":"10.1126\/sciadv.aaw6671","volume":"5","author":"M Huelsmann","year":"2019","unstructured":"Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Sci Adv. 2019;5(9):eaaw6671.","journal-title":"Sci Adv"},{"issue":"1","key":"1243_CR35","doi-asserted-by":"publisher","first-page":"17446","DOI":"10.1038\/s41598-017-17782-4","volume":"7","author":"J Lachner","year":"2017","unstructured":"Lachner J, Mlitz V, Tschachler E, Eckhart L. Epidermal cornification is preceded by the expression of a keratinocyte-specific set of pyroptosis-related genes. Sci Rep. 2017;7(1):17446.","journal-title":"Sci Rep"},{"key":"1243_CR36","doi-asserted-by":"publisher","first-page":"592375","DOI":"10.3389\/fmars.2020.592375","volume":"7","author":"G Espregueira Themudo","year":"2020","unstructured":"Espregueira Themudo G, Alves LQ, Machado AM, Lopes-Marques M, da Fonseca RR, Fonseca M, et al. Losing genes: the evolutionary remodeling of cetacea skin. Front Mar Sci. 2020;7:592375.","journal-title":"Front Mar Sci"},{"issue":"8","key":"1243_CR37","doi-asserted-by":"publisher","first-page":"3036","DOI":"10.1073\/pnas.1818504116","volume":"116","author":"N Hecker","year":"2019","unstructured":"Hecker N, Sharma V, Hiller M. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. Proc Natl Acad Sci U S A. 2019;116(8):3036\u201341.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"1243_CR38","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1086\/302219","volume":"64","author":"MV Olson","year":"1999","unstructured":"Olson MV. When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet. 1999;64(1):18\u201323.","journal-title":"Am J Hum Genet"},{"key":"1243_CR39","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.ympev.2014.05.016","volume":"78","author":"CA Emerling","year":"2014","unstructured":"Emerling CA, Springer MS. Eyes underground: regression of visual protein networks in subterranean mammals. Mol Phylogenet Evol. 2014;78:260\u201370.","journal-title":"Mol Phylogenet Evol"},{"issue":"8","key":"1243_CR40","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1093\/molbev\/msw098","volume":"33","author":"X Prudent","year":"2016","unstructured":"Prudent X, Parra G, Schwede P, Roscito JG, Hiller M. Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species\u2019 phenotypic and genomic differences. Mol Biol Evol. 2016;33(8):2135\u201350.","journal-title":"Mol Biol Evol"},{"issue":"3","key":"1243_CR41","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1093\/icb\/icy004","volume":"58","author":"CA Emerling","year":"2018","unstructured":"Emerling CA. Regressed but not gone: patterns of vision gene loss and retention in subterranean mammals. Integr Comp Biol. 2018;58(3):441\u201351.","journal-title":"Integr Comp Biol"},{"issue":"10","key":"1243_CR42","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.tig.2008.08.005","volume":"24","author":"T Vavouri","year":"2008","unstructured":"Vavouri T, Semple JI, Lehner B. Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet. 2008;24(10):485\u20138.","journal-title":"Trends Genet"},{"issue":"10","key":"1243_CR43","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni M, Berkeley MR, Seppey M, Simao FA, Zdobnov EM. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647\u201354.","journal-title":"Mol Biol Evol"},{"issue":"11","key":"1243_CR44","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1016\/j.exger.2007.09.004","volume":"42","author":"TW Mitchell","year":"2007","unstructured":"Mitchell TW, Buffenstein R, Hulbert AJ. Membrane phospholipid composition may contribute to exceptional longevity of the naked mole-rat (Heterocephalus glaber): a comparative study using shotgun lipidomics. Exp Gerontol. 2007;42(11):1053\u201362.","journal-title":"Exp Gerontol"},{"issue":"10","key":"1243_CR45","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1038\/ncb1969","volume":"11","author":"M Melixetian","year":"2009","unstructured":"Melixetian M, Klein DK, Sorensen CS, Helin K. NEK11 regulates CDC25A degradation and the IR-induced G2\/M checkpoint. Nat Cell Biol. 2009;11(10):1247\u201353.","journal-title":"Nat Cell Biol"},{"issue":"18","key":"1243_CR46","doi-asserted-by":"publisher","first-page":"2659","DOI":"10.1038\/onc.2010.19","volume":"29","author":"Z Li","year":"2010","unstructured":"Li Z, Zhang Q, Mao JH, Weise A, Mrasek K, Fan X, et al. An HDAC1-binding domain within FATS bridges p21 turnover to radiation-induced tumorigenesis. Oncogene. 2010;29(18):2659\u201371.","journal-title":"Oncogene"},{"key":"1243_CR47","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1186\/1476-4598-9-244","volume":"9","author":"X Zhang","year":"2010","unstructured":"Zhang X, Zhang Q, Zhang J, Qiu L, Yan SS, Feng J, et al. FATS is a transcriptional target of p53 and associated with antitumor activity. Mol Cancer. 2010;9:244.","journal-title":"Mol Cancer"},{"issue":"47","key":"1243_CR48","doi-asserted-by":"publisher","first-page":"5424","DOI":"10.1038\/onc.2013.494","volume":"33","author":"S Yan","year":"2014","unstructured":"Yan S, Qiu L, Ma K, Zhang X, Zhao Y, Zhang J, et al. FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage. Oncogene. 2014;33(47):5424\u201333.","journal-title":"Oncogene"},{"issue":"3","key":"1243_CR49","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.celrep.2018.06.061","volume":"24","author":"KP Bhat","year":"2018","unstructured":"Bhat KP, Krishnamoorthy A, Dungrawala H, Garcin EB, Modesti M, Cortez D. RADX modulates RAD51 activity to control replication fork protection. Cell Rep. 2018;24(3):538\u201345.","journal-title":"Cell Rep"},{"issue":"7644","key":"1243_CR50","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nature21358","volume":"543","author":"P Drane","year":"2017","unstructured":"Drane P, Brault ME, Cui G, Meghani K, Chaubey S, Detappe A, et al. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature. 2017;543(7644):211\u20136.","journal-title":"Nature"},{"issue":"9","key":"1243_CR51","doi-asserted-by":"publisher","first-page":"5846","DOI":"10.1093\/nar\/gku237","volume":"42","author":"T Amangyeld","year":"2014","unstructured":"Amangyeld T, Shin YK, Lee M, Kwon B, Seo YS. Human MUS81-EME2 can cleave a variety of DNA structures including intact Holliday junction and nicked duplex. Nucleic Acids Res. 2014;42(9):5846\u201362.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1243_CR52","doi-asserted-by":"publisher","first-page":"3833","DOI":"10.1093\/nar\/gkt1333","volume":"42","author":"A Pepe","year":"2014","unstructured":"Pepe A, West SC. Substrate specificity of the MUS81-EME2 structure selective endonuclease. Nucleic Acids Res. 2014;42(6):3833\u201345.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1243_CR53","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1016\/j.celrep.2015.12.093","volume":"14","author":"H Techer","year":"2016","unstructured":"Techer H, Koundrioukoff S, Carignon S, Wilhelm T, Millot GA, Lopez BS, et al. Signaling from Mus81-Eme2-dependent DNA damage elicited by Chk1 deficiency modulates replication fork speed and origin usage. Cell Rep. 2016;14(5):1114\u201327.","journal-title":"Cell Rep"},{"issue":"4","key":"1243_CR54","doi-asserted-by":"publisher","first-page":"31","DOI":"10.32607\/20758251-2017-9-4-31-41","volume":"9","author":"IO Petruseva","year":"2017","unstructured":"Petruseva IO, Evdokimov AN, Lavrik OI. Genome stability maintenance in naked mole-rat. Acta Naturae. 2017;9(4):31\u201341.","journal-title":"Acta Naturae"},{"issue":"8","key":"1243_CR55","doi-asserted-by":"publisher","first-page":"jeb174540","DOI":"10.1242\/jeb.174540","volume":"221","author":"V Domankevich","year":"2018","unstructured":"Domankevich V, Eddini H, Odeh A, Shams I. Resistance to DNA damage and enhanced DNA repair capacity in the hypoxia-tolerant blind mole rat Spalax carmeli. J Exp Biol. 2018;221(8):jeb174540.","journal-title":"J Exp Biol"},{"issue":"10","key":"1243_CR56","doi-asserted-by":"publisher","first-page":"e1008354","DOI":"10.1371\/journal.pgen.1008354","volume":"15","author":"P Gan","year":"2019","unstructured":"Gan P, Patterson M, Velasquez A, Wang K, Tian D, Windle JJ, et al. Tnni3k alleles influence ventricular mononuclear diploid cardiomyocyte frequency. Plos Genet. 2019;15(10):e1008354.","journal-title":"Plos Genet"},{"issue":"11","key":"1243_CR57","doi-asserted-by":"publisher","first-page":"4852","DOI":"10.1248\/cpb.34.4852","volume":"34","author":"T Aoyagi","year":"1986","unstructured":"Aoyagi T, Wada T, Kojima F, Nagai M, Harada S, Hachisu M, et al. Inhibitors of aminopeptidase B suppress the development of hypertension in spontaneously hypertensive rats. Chem Pharm Bull (Tokyo). 1986;34(11):4852\u20134.","journal-title":"Chem Pharm Bull (Tokyo)"},{"issue":"17","key":"1243_CR58","doi-asserted-by":"publisher","first-page":"2642","DOI":"10.1161\/CIRCULATIONAHA.105.540500","volume":"112","author":"BA Borlaug","year":"2005","unstructured":"Borlaug BA, Melenovsky V, Marhin T, Fitzgerald P, Kass DA. Sildenafil inhibits beta-adrenergic-stimulated cardiac contractility in humans. Circulation. 2005;112(17):2642\u20139.","journal-title":"Circulation"},{"issue":"2","key":"1243_CR59","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1590\/1414-431X20122515","volume":"46","author":"H Wang","year":"2013","unstructured":"Wang H, Wang L, Song L, Zhang YW, Ye J, Xu RX, et al. TNNI3K is a novel mediator of myofilament function and phosphorylates cardiac troponin I. Braz J Med Biol Res. 2013;46(2):128\u201337.","journal-title":"Braz J Med Biol Res"},{"issue":"1","key":"1243_CR60","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1086\/physzool.54.1.30155800","volume":"54","author":"R Arieli","year":"1981","unstructured":"Arieli R, Ar A. Heart-rate responses of the mole rat (Spalax-Ehrenbergi) in hypercapnic, hypoxic, and cold conditions. Physiol Zool. 1981;54(1):14\u201321.","journal-title":"Physiol Zool"},{"issue":"5","key":"1243_CR61","doi-asserted-by":"publisher","first-page":"H730","DOI":"10.1152\/ajpheart.00831.2013","volume":"306","author":"KM Grimes","year":"2014","unstructured":"Grimes KM, Voorhees A, Chiao YA, Han HC, Lindsey ML, Buffenstein R. Cardiac function of the naked mole-rat: ecophysiological responses to working underground. Am J Physiol Heart Circ Physiol. 2014;306(5):H730\u20137.","journal-title":"Am J Physiol Heart Circ Physiol"},{"issue":"3","key":"1243_CR62","doi-asserted-by":"publisher","first-page":"H284","DOI":"10.1152\/ajpheart.00305.2014","volume":"307","author":"KM Grimes","year":"2014","unstructured":"Grimes KM, Reddy AK, Lindsey ML, Buffenstein R. And the beat goes on: maintained cardiovascular function during aging in the longest-lived rodent, the naked mole-rat. Am J Physiol Heart Circ Physiol. 2014;307(3):H284\u201391.","journal-title":"Am J Physiol Heart Circ Physiol"},{"issue":"2","key":"1243_CR63","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nm1175","volume":"11","author":"E Takimoto","year":"2005","unstructured":"Takimoto E, Champion HC, Li M, Belardi D, Ren S, Rodriguez ER, et al. Chronic inhibition of cyclic GMP phosphodiesterase 5A prevents and reverses cardiac hypertrophy. Nat Med. 2005;11(2):214\u201322.","journal-title":"Nat Med"},{"issue":"5","key":"1243_CR64","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1161\/HYPERTENSIONAHA.107.087759","volume":"49","author":"NG Perez","year":"2007","unstructured":"Perez NG, Piaggio MR, Ennis IL, Garciarena CD, Morales C, Escudero EM, et al. Chiappe de Cingolani G, Yang XP, Cingolani HE: Phosphodiesterase 5A inhibition induces Na+\/H+ exchanger blockade and protection against myocardial infarction. Hypertension. 2007;49(5):1095\u2013103.","journal-title":"Hypertension"},{"issue":"4","key":"1243_CR65","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1161\/CIRCHEARTFAILURE.108.796789","volume":"1","author":"RJ Tedford","year":"2008","unstructured":"Tedford RJ, Hemnes AR, Russell SD, Wittstein IS, Mahmud M, Zaiman AL, et al. PDE5A inhibitor treatment of persistent pulmonary hypertension after mechanical circulatory support. Circ Heart Fail. 2008;1(4):213\u20139.","journal-title":"Circ Heart Fail"},{"issue":"19","key":"1243_CR66","doi-asserted-by":"publisher","first-page":"2323","DOI":"10.1161\/CIRCULATIONAHA.111.063412","volume":"125","author":"E Giannetta","year":"2012","unstructured":"Giannetta E, Isidori AM, Galea N, Carbone I, Mandosi E, Vizza CD, et al. Chronic inhibition of cGMP phosphodiesterase 5A improves diabetic cardiomyopathy: A randomized, controlled clinical trial using magnetic resonance imaging with myocardial tagging. Circulation. 2012;125(19):2323\u201333.","journal-title":"Circulation"},{"issue":"207","key":"1243_CR67","doi-asserted-by":"publisher","first-page":"207ra141","DOI":"10.1126\/scitranslmed.3006479","volume":"5","author":"RJ Vagnozzi","year":"2013","unstructured":"Vagnozzi RJ, Gatto GJ Jr, Kallander LS, Hoffman NE, Mallilankaraman K, Ballard VL, et al. Inhibition of the cardiomyocyte-specific kinase TNNI3K limits oxidative stress, injury, and adverse remodeling in the ischemic heart. Sci Transl Med. 2013;5(207):207ra141.","journal-title":"Sci Transl Med"},{"issue":"9","key":"1243_CR68","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1038\/ng.3929","volume":"49","author":"M Patterson","year":"2017","unstructured":"Patterson M, Barske L, Van Handel B, Rau CD, Gan P, Sharma A, et al. Frequency of mononuclear diploid cardiomyocytes underlies natural variation in heart regeneration. Nat Genet. 2017;49(9):1346\u201353.","journal-title":"Nat Genet"},{"issue":"6402","key":"1243_CR69","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1126\/science.aap7714","volume":"361","author":"WK Meyer","year":"2018","unstructured":"Meyer WK, Jamison J, Richter R, Woods SE, Partha R, Kowalczyk A, et al. Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. Science. 2018;361(6402):591\u20134.","journal-title":"Science"},{"issue":"9","key":"1243_CR70","doi-asserted-by":"publisher","first-page":"5407","DOI":"10.1167\/iovs.15-16647","volume":"56","author":"JD Deming","year":"2015","unstructured":"Deming JD, Pak JS, Brown BM, Kim MK, Aung MH, Eom YS, et al. Visual cone arrestin 4 contributes to visual function and cone health. Invest Ophthalmol Vis Sci. 2015;56(9):5407\u201316.","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"D1","key":"1243_CR71","doi-asserted-by":"publisher","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","volume":"45","author":"J MacArthur","year":"2017","unstructured":"MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res. 2017;45(D1):D896\u2013901.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"1243_CR72","doi-asserted-by":"publisher","first-page":"e79629","DOI":"10.1371\/journal.pone.0079629","volume":"8","author":"X Deng","year":"2013","unstructured":"Deng X, Sabino EC, Cunha-Neto E, Ribeiro AL, Ianni B, Mady C, et al. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. Plos One. 2013;8(11):e79629.","journal-title":"Plos One"},{"issue":"10","key":"1243_CR73","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.1038\/s41588-018-0205-x","volume":"50","author":"E Evangelou","year":"2018","unstructured":"Evangelou E, Warren HR, Mosen-Ansorena D, Mifsud B, Pazoki R, Gao H, et al. Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits. Nat genet. 2018;50(10):1412\u201325.","journal-title":"Nat genet"},{"issue":"6","key":"1243_CR74","doi-asserted-by":"publisher","first-page":"e0198166","DOI":"10.1371\/journal.pone.0198166","volume":"13","author":"MF Feitosa","year":"2018","unstructured":"Feitosa MF, Kraja AT, Chasman DI, Sung YJ, Winkler TW, Ntalla I, et al. Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. Plos One. 2018;13(6):e0198166.","journal-title":"Plos One"},{"issue":"1","key":"1243_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-018-04148-1","volume":"9","author":"J Ram\u00edrez","year":"2018","unstructured":"Ram\u00edrez J, van Duijvenboden S, Ntalla I, Mifsud B, Warren HR, Tzanis E, et al. Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system. Nat Commun. 2018;9(1):1\u201310.","journal-title":"Nat Commun"},{"issue":"1","key":"1243_CR76","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/s41588-018-0303-9","volume":"51","author":"A Giri","year":"2019","unstructured":"Giri A, Hellwege JN, Keaton JM, Park J, Qiu C, Warren HR, et al. Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. Nat Genet. 2019;51(1):51\u201362.","journal-title":"Nat Genet"},{"issue":"12","key":"1243_CR77","doi-asserted-by":"publisher","first-page":"1928","DOI":"10.1038\/cdd.2010.73","volume":"17","author":"I Lassot","year":"2010","unstructured":"Lassot I, Robbins I, Kristiansen M, Rahmeh R, Jaudon F, Magiera MM, et al. Trim17, a novel E3 ubiquitin-ligase, initiates neuronal apoptosis. Cell Death Differ. 2010;17(12):1928\u201341.","journal-title":"Cell Death Differ"},{"issue":"1","key":"1243_CR78","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1146\/annurev.physiol.69.031905.163111","volume":"69","author":"JM Ramirez","year":"2007","unstructured":"Ramirez JM, Folkow LP, Blix AS. Hypoxia tolerance in mammals and birds: from the wilderness to the clinic. Annu Rev Physiol. 2007;69(1):113\u201343.","journal-title":"Annu Rev Physiol"},{"issue":"38","key":"1243_CR79","doi-asserted-by":"publisher","first-page":"11905","DOI":"10.1073\/pnas.1514896112","volume":"112","author":"K Li","year":"2015","unstructured":"Li K, Hong W, Jiao H, Wang GD, Rodriguez KA, Buffenstein R, et al. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax. Proc Natl Acad Sci U S A. 2015;112(38):11905\u201310.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"1243_CR80","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0034-5687(86)90064-2","volume":"64","author":"RE Weber","year":"1986","unstructured":"Weber RE, Heath ME, White FN. Oxygen binding functions of blood and hemoglobin from the Chinese pangolin, Manis pentadactyla: possible implications of burrowing and low body temperature. Respir Physiol. 1986;64(1):103\u201312.","journal-title":"Respir Physiol"},{"issue":"10","key":"1243_CR81","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1101\/gr.203521.115","volume":"26","author":"SW Choo","year":"2016","unstructured":"Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, et al. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res. 2016;26(10):1312\u201322.","journal-title":"Genome Res"},{"issue":"2","key":"1243_CR82","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/cdd.2012.124","volume":"20","author":"MM Magiera","year":"2013","unstructured":"Magiera MM, Mora S, Mojsa B, Robbins I, Lassot I, Desagher S. Trim17-mediated ubiquitination and degradation of Mcl-1 initiate apoptosis in neurons. Cell Death Differ. 2013;20(2):281\u201392.","journal-title":"Cell Death Differ"},{"key":"1243_CR83","doi-asserted-by":"publisher","first-page":"747737","DOI":"10.3389\/fimmu.2021.747737","volume":"12","author":"A Agueda-Pinto","year":"2021","unstructured":"Agueda-Pinto A, Alves LQ, Neves F, McFadden G, Jacobs BL, Castro LFC, et al. Convergent loss of the necroptosis pathway in disparate mammalian lineages shapes viruses countermeasures. Front Immunol. 2021;12:747737.","journal-title":"Front Immunol"},{"issue":"6","key":"1243_CR84","doi-asserted-by":"publisher","first-page":"1270","DOI":"10.1093\/molbev\/msz068","volume":"36","author":"M Lopes-Marques","year":"2019","unstructured":"Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding M-HS, et al. Complete inactivation of sebum-producing genes parallels the loss of sebaceous glands in Cetacea. Mol Biol Evol. 2019;36(6):1270\u201380.","journal-title":"Mol Biol Evol"},{"issue":"3","key":"1243_CR85","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1371\/journal.pbio.0040052","volume":"4","author":"X Wang","year":"2006","unstructured":"Wang X, Grus WE, Zhang J. Gene losses during human origins. Plos Biol. 2006;4(3):e52.","journal-title":"Plos Biol"},{"issue":"5780","key":"1243_CR86","doi-asserted-by":"publisher","first-page":"1614","DOI":"10.1126\/science.1124309","volume":"312","author":"PC Sabeti","year":"2006","unstructured":"Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, et al. Positive natural selection in the human lineage. Science. 2006;312(5780):1614\u201320.","journal-title":"Science"},{"issue":"2","key":"1243_CR87","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1093\/biolre\/ioz103","volume":"101","author":"Y Lu","year":"2019","unstructured":"Lu Y, Oura S, Matsumura T, Oji A, Sakurai N, Fujihara Y, et al. CRISPR\/Cas9-mediated genome editing reveals 30 testis-enriched genes dispensable for male fertility in mice. Biol Reprod. 2019;101(2):501\u201311.","journal-title":"Biol Reprod"},{"issue":"1","key":"1243_CR88","doi-asserted-by":"publisher","first-page":"47","DOI":"10.7555\/JBR.34.20200069","volume":"35","author":"X He","year":"2021","unstructured":"He X, Xie W, Li H, Cui Y, Wang Y, Guo X, et al. The testis-specifically expressed gene Trim69 is not essential for fertility in mice. J Biomed Res. 2021;35(1):47\u201360.","journal-title":"J Biomed Res"},{"issue":"11","key":"1243_CR89","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1038\/cdd.2014.121","volume":"21","author":"J Liu","year":"2014","unstructured":"Liu J, Zhang C, Wang XL, Ly P, Belyi V, Xu-Monette ZY, et al. E3 ubiquitin ligase TRIM32 negatively regulates tumor suppressor p53 to promote tumorigenesis. Cell Death Differ. 2014;21(11):1792\u2013804.","journal-title":"Cell Death Differ"},{"issue":"5770","key":"1243_CR90","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1126\/science.1123539","volume":"312","author":"DM Weinreich","year":"2006","unstructured":"Weinreich DM, Delaney NF, Depristo MA, Hartl DL. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science. 2006;312(5770):111\u20134.","journal-title":"Science"},{"issue":"8","key":"1243_CR91","doi-asserted-by":"publisher","first-page":"e1001935","DOI":"10.1371\/journal.pbio.1001935","volume":"12","author":"B Szamecz","year":"2014","unstructured":"Szamecz B, Boross G, Kalapis D, Kovacs K, Fekete G, Farkas Z, et al. The genomic landscape of compensatory evolution. Plos Biol. 2014;12(8):e1001935.","journal-title":"Plos Biol"},{"key":"1243_CR92","unstructured":"The Ensembl database. http:\/\/useast.ensembl.org\/index.html. Accessed Oct 2014."},{"key":"1243_CR93","unstructured":"The NCBI database. https:\/\/www.ncbi.nlm.nih.gov. Accessed Oct 2014"},{"issue":"4","key":"1243_CR94","first-page":"656","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12(4):656\u201364.","journal-title":"Genome Res"},{"issue":"1","key":"1243_CR95","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1101\/gr.082081.108","volume":"19","author":"R She","year":"2009","unstructured":"She R, Chu JS, Wang K, Pei J, Chen N. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 2009;19(1):143\u20139.","journal-title":"Genome Res"},{"issue":"5","key":"1243_CR96","doi-asserted-by":"publisher","first-page":"988","DOI":"10.1101\/gr.1865504","volume":"14","author":"E Birney","year":"2004","unstructured":"Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome Res. 2004;14(5):988\u201395.","journal-title":"Genome Res"},{"issue":"3","key":"1243_CR97","doi-asserted-by":"publisher","first-page":"R26","DOI":"10.1186\/gb-2010-11-3-r26","volume":"11","author":"ZD Zhang","year":"2010","unstructured":"Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol. 2010;11(3):R26.","journal-title":"Genome Biol"},{"issue":"6070","key":"1243_CR98","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1126\/science.1215040","volume":"335","author":"DG MacArthur","year":"2012","unstructured":"MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012;335(6070):823\u20138.","journal-title":"Science"},{"issue":"24","key":"1243_CR99","doi-asserted-by":"publisher","first-page":"3985","DOI":"10.1093\/bioinformatics\/btx527","volume":"33","author":"V Sharma","year":"2017","unstructured":"Sharma V, Schwede P, Hiller M. CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation. Bioinformatics. 2017;33(24):3985\u20137.","journal-title":"Bioinformatics"},{"key":"1243_CR100","unstructured":"Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Bioproject. 2011; https:\/\/identifiers.org\/GEO\/GSE30337."},{"key":"1243_CR101","unstructured":"Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Bioproject. 2011; https:\/\/identifiers.org\/bioproject\/PRJNA68323."},{"key":"1243_CR102","doi-asserted-by":"crossref","unstructured":"Li K-X, Hong W, Jiao H-W, Wang G-D, Rodriguez KA, Buffenstein R, et al. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax. Bioproject https:\/\/identifiers.org\/bioproject\/PRJNA285131. 2015.","DOI":"10.1073\/pnas.1514896112"},{"issue":"3","key":"1243_CR103","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1093\/molbev\/msu400","volume":"32","author":"JO Wertheim","year":"2015","unstructured":"Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol. 2015;32(3):820\u201332.","journal-title":"Mol Biol Evol"},{"issue":"30","key":"1243_CR104","doi-asserted-by":"publisher","first-page":"10557","DOI":"10.1073\/pnas.0409137102","volume":"102","author":"A Loytynoja","year":"2005","unstructured":"Loytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A. 2005;102(30):10557\u201362.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"1243_CR105","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","volume":"17","author":"J Castresana","year":"2000","unstructured":"Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540\u201352.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"1243_CR106","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1038\/s41401-018-0064-0","volume":"40","author":"DK Guo","year":"2019","unstructured":"Guo DK, Zhu Y, Sun HY, Xu XY, Zhang S, Hao ZB, et al. Pharmacological activation of REV-ERB\u03b1 represses LPS-induced microglial activation through the NF-\u03baB pathway. Acta Pharmacol Sin. 2019;40(1):26\u201334.","journal-title":"Acta Pharmacol Sin"},{"issue":"2","key":"1243_CR107","doi-asserted-by":"publisher","first-page":"195","DOI":"10.4062\/biomolther.2020.089","volume":"29","author":"W Yu","year":"2021","unstructured":"Yu W, Wang B, Zhou L, Xu G. Endoplasmic reticulum stress-mediated p62 downregulation inhibits apoptosis via c-Jun upregulation. Biomol Ther (Seoul). 2021;29(2):195\u2013204.","journal-title":"Biomol Ther (Seoul)"},{"issue":"11","key":"1243_CR108","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1038\/s41401-019-0286-9","volume":"40","author":"X Shen","year":"2019","unstructured":"Shen X, Zhao YF, Xu SQ, Wang L, Cao HM, Cao Y, et al. Cathepsin L induced PC-12 cell apoptosis via activation of B-Myb and regulation of cell cycle proteins. Acta Pharmacol Sin. 2019;40(11):1394\u2013403.","journal-title":"Acta Pharmacol Sin"}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-022-01243-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-022-01243-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-022-01243-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,23]],"date-time":"2022-10-23T17:06:12Z","timestamp":1666544772000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-022-01243-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,17]]},"references-count":108,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["1243"],"URL":"https:\/\/doi.org\/10.1186\/s12915-022-01243-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.28.446201","asserted-by":"object"}]},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,17]]},"assertion":[{"value":"22 September 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 January 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","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 that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"44"}}