{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:13:54Z","timestamp":1792782834706,"version":"4.5.0"},"reference-count":53,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"China Scholarship Council","award":["No.202109307003"],"award-info":[{"award-number":["No.202109307003"]}],"id":[{"id":"https:\/\/ror.org\/04atp4p48","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["No. 2025ZB666"],"award-info":[{"award-number":["No. 2025ZB666"]}]},{"DOI":"10.13039\/501100000040","name":"Agriculture and Agri-Food Canada","doi-asserted-by":"publisher","award":["J-002223"],"award-info":[{"award-number":["J-002223"]}],"id":[{"id":"10.13039\/501100000040","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Retrotransposons are major components of mammalian genomes, yet their genome-wide annotation and epigenetic regulation in cattle remain incompletely characterized. Here, we present a comprehensive annotation and integrative epigenomic analysis of major retrotransposon classes in the bovine genome, with emphasis on DNA methylation patterns and their potential roles in subclinical mastitis. Using a multi-step\n                    <jats:italic>de novo<\/jats:italic>\n                    pipeline, we identified and classified long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) in the bovine reference genome, including three LINE families, seven SINE families, and 20 ERV families. Retrotransposons accounted for ~\u200940% of the genome, with LINEs representing the largest fraction. Evolutionary analysis suggested that BosL1A1, BosSINEL, BosERV1, and BosERV16 are the most recently active families. DNA methylation profiles in milk somatic cells showed consistently high levels across retrotransposons, with widespread hypermethylation in cows with\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    \u2013induced subclinical mastitis. We identified 20,839 differentially methylated retrotransposons, 3,306 of which overlapped differentially expressed genes. Promoter- and exon-overlapping elements showed inverse correlations between methylation and gene expression, and enriched genes are involved in immune and transport pathways. These results provide a comprehensive bovine mobilome resource and indicate that retrotransposon methylation is associated with gene regulation and host responses to mastitis.\n                  <\/jats:p>","DOI":"10.1007\/s10142-026-01970-5","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T06:45:13Z","timestamp":1789541113000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A comprehensive map of the bovine mobilome and their epigenetic regulation of mastitis"],"prefix":"10.1007","volume":"26","author":[{"given":"Naisu","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6067-6067","authenticated-orcid":false,"given":"Mengqi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E.","family":"Abanda Mbili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antony T.","family":"Vincent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengyi","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8810-9294","authenticated-orcid":false,"given":"Eveline M.","family":"Ibeagha-Awemu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"issue":"31","key":"1970_CR1","doi-asserted-by":"publisher","first-page":"12855","DOI":"10.1073\/pnas.0901282106","volume":"106","author":"DL Adelson","year":"2009","unstructured":"Adelson DL, Raison JM, Edgar RC (2009) Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Natl Acad Sci USA 106(31):12855\u201312860","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"1970_CR2","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1186\/s12864-025-11740-5","volume":"26","author":"S An","year":"2025","unstructured":"An S, Mi S, Chen S, Tang Y, Xing Y, Jing Y, and Y. Yu (2025) Unraveling key transposable elements in pathogen-induced bovine mastitis through comparative in vivo and in vitro transcriptomic analysis. BMC Genomics 26(1):611","journal-title":"BMC Genomics"},{"issue":"1","key":"1970_CR3","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s13072-018-0205-1","volume":"11","author":"D Anastasiadi","year":"2018","unstructured":"Anastasiadi D, Esteve-Codina A, Piferrer F (2018) Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics chromatin 11(1):37","journal-title":"Epigenetics chromatin"},{"issue":"8","key":"1970_CR4","first-page":"1091","volume":"25","author":"G Bindea","year":"2009","unstructured":"Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pag\u00e8s F, Trajanoski Z, Galon J (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinf (Oxford England) 25(8):1091\u20131093","journal-title":"Bioinf (Oxford England)"},{"issue":"1795","key":"1970_CR5","doi-asserted-by":"publisher","first-page":"20190332","DOI":"10.1098\/rstb.2019.0332","volume":"375","author":"L Bogdan","year":"2020","unstructured":"Bogdan L, Barreiro L, Bourque G (2020) Transposable elements have contributed human regulatory regions that are activated upon bacterial infection. Ser B Biol Sci 375(1795):20190332Philosophical transactions of the Royal Society of London","journal-title":"Ser B Biol Sci"},{"issue":"1","key":"1970_CR6","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","volume":"19","author":"G Bourque","year":"2018","unstructured":"Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsv\u00e1k Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C (2018) Ten things you should know about transposable elements. Genome Biol 19(1):199","journal-title":"Genome Biol"},{"issue":"1","key":"1970_CR7","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s13100-019-0161-8","volume":"10","author":"C Chen","year":"2019","unstructured":"Chen C, Wang W, Wang X, Shen D, Wang S, Wang Y, Gao B, Wimmers K, Mao J, Li K, Song C (2019) Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mob DNA 10(1):19","journal-title":"Mob DNA"},{"issue":"3","key":"1970_CR10","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/ng.2553","volume":"45","author":"EB Chuong","year":"2013","unstructured":"Chuong EB, Rumi MA, Soares MJ, Baker JC (2013) Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45(3):325\u2013329","journal-title":"Nat Genet"},{"key":"1970_CR8","doi-asserted-by":"crossref","unstructured":"Chuong EB, Elde NC, Feschotte C (2016) Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science (New York, N.Y.) 351(6277):1083\u20131087","DOI":"10.1126\/science.aad5497"},{"issue":"2","key":"1970_CR9","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nrg.2016.139","volume":"18","author":"EB Chuong","year":"2017","unstructured":"Chuong EB, Elde NC, Feschotte C (2017) Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet 18(2):71\u201386","journal-title":"Nat Rev Genet"},{"issue":"10","key":"1970_CR11","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/nrg2640","volume":"10","author":"R Cordaux","year":"2009","unstructured":"Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10(10):691\u2013703","journal-title":"Nat Rev Genet"},{"issue":"7","key":"1970_CR12","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/s41576-019-0106-6","volume":"20","author":"\u00d6 Deniz","year":"2019","unstructured":"Deniz \u00d6, Frost JM, Branco MR (2019) Regulation of transposable elements by DNA modifications. Nat Rev Genet 20(7):417\u2013431","journal-title":"Nat Rev Genet"},{"issue":"50","key":"1970_CR13","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.21105\/joss.02170","volume":"5","author":"H-G Drost","year":"2020","unstructured":"Drost H-G (2020) LTRpred: de novo annotation of intact retrotransposons. J Open Source Softw 5(50):2170","journal-title":"J Open Source Softw"},{"issue":"6","key":"1970_CR14","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1016\/j.devcel.2016.02.024","volume":"36","author":"G Ecco","year":"2016","unstructured":"Ecco G, Cassano M, Kauzlaric A, Duc J, Coluccio A, Offner S, Imbeault M, Rowe HM, Turelli P, Trono D (2016) Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues. Dev Cell 36(6):611\u2013623","journal-title":"Dev Cell"},{"key":"1970_CR15","first-page":"aac7247","volume-title":"Retrotransposons as regulators of gene expression","author":"RA Elbarbary","year":"2016","unstructured":"Elbarbary RA, Lucas BA, Maquat LE (2016) Retrotransposons as regulators of gene expression, vol 351. Science, New York, N.Y., p aac7247. 6274"},{"key":"1970_CR16","doi-asserted-by":"crossref","unstructured":"Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA 117(17):9451\u20139457","DOI":"10.1073\/pnas.1921046117"},{"issue":"7","key":"1970_CR17","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1261\/rna.078721.121","volume":"27","author":"A G\u00e1zquez-Guti\u00e9rrez","year":"2021","unstructured":"G\u00e1zquez-Guti\u00e9rrez A, Witteveldt J, Heras SR, Macias S (2021) Sensing of transposable elements by the antiviral innate immune system. RNA (New York N Y) 27(7):735\u2013752","journal-title":"RNA (New York N Y)"},{"issue":"11","key":"1970_CR18","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1038\/s41576-018-0050-x","volume":"19","author":"P Goerner-Potvin","year":"2018","unstructured":"Goerner-Potvin P, Bourque G (2018) Computational tools to unmask transposable elements. Nat Rev Genet 19(11):688\u2013704","journal-title":"Nat Rev Genet"},{"issue":"1","key":"1970_CR19","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1186\/s12864-021-08117-9","volume":"22","author":"MA Ibrahim","year":"2021","unstructured":"Ibrahim MA, Al-Shomrani BM, Simenc M, Alharbi SN, Alqahtani FH, Al-Fageeh MB, Manee MM (2021) Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus. BMC Genomics 22(1):842","journal-title":"BMC Genomics"},{"issue":"10","key":"1970_CR20","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1038\/s41580-025-00867-8","volume":"26","author":"\u0130A Il\u0131k","year":"2025","unstructured":"Il\u0131k \u0130A, Yang X, Zhang ZZZ, Akta\u015f T (2025) Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease. Nat Rev Mol Cell Biol 26(10):759\u2013775","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"6","key":"1970_CR21","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1042\/EBC20190039","volume":"63","author":"N Jansz","year":"2019","unstructured":"Jansz N (2019) DNA methylation dynamics at transposable elements in mammals. Essays Biochem 63(6):677\u2013689","journal-title":"Essays Biochem"},{"issue":"8","key":"1970_CR22","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1101\/gr.276241.121","volume":"32","author":"CJ Kelly","year":"2022","unstructured":"Kelly CJ, Chitko-McKown CG, Chuong EB (2022) Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity. Genome Res 32(8):1474\u20131486","journal-title":"Genome Res"},{"issue":"2","key":"1970_CR23","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/BF01731581","volume":"16","author":"M Kimura","year":"1980","unstructured":"Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J J Mol Evol 16(2):111\u2013120","journal-title":"J J Mol Evol"},{"key":"1970_CR24","doi-asserted-by":"crossref","unstructured":"Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD (2007) Clustal W and Clustal X version 2.0. bioinformatics. 23(21):2947-8.","DOI":"10.1093\/bioinformatics\/btm404"},{"issue":"3","key":"1970_CR25","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nrg2719","volume":"11","author":"JA Law","year":"2010","unstructured":"Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204\u2013220","journal-title":"Nat Rev Genet"},{"issue":"16","key":"1970_CR26","first-page":"2502","volume":"32","author":"H Lee","year":"2016","unstructured":"Lee H, Lee M, Mohammed Ismail W, Rho M, Fox GC, Oh S, Tang H (2016) MGEScan: a Galaxy-based system for identifying retrotransposons in genomes. Bioinf (Oxford England) 32(16):2502\u20132504","journal-title":"Bioinf (Oxford England)"},{"key":"1970_CR27","doi-asserted-by":"publisher","first-page":"1544330","DOI":"10.3389\/fgene.2025.1544330","volume":"16","author":"MD Li","year":"2025","unstructured":"Li MD, Li HR, Ye SH (2025) Multi-tissue transcriptomic characterization of endogenous retrovirus-derived transcripts in Capra hircus. Front Genet 16:1544330","journal-title":"Front Genet"},{"issue":"17","key":"1970_CR28","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1093\/nar\/gkab563","volume":"49","author":"X Liao","year":"2021","unstructured":"Liao X, Li M, Hu K, Wu FX, Gao X, Wang J (2021) A sensitive repeat identification framework based on short and long reads. Nucleic Acids Res 49(17):e100","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1970_CR29","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1471-2164-7-140","volume":"7","author":"GE Liu","year":"2006","unstructured":"Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP (2006) Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics 7(1):140","journal-title":"BMC Genomics"},{"issue":"1","key":"1970_CR30","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/s41597-020-0400-3","volume":"7","author":"Y Liu","year":"2020","unstructured":"Liu Y, Luo J, Dou J, Yan B, Ren Q, Tang B, Wang K, Qiu Q (2020) The sequence and de novo assembly of the wild yak genome. Sci Data 7(1):66","journal-title":"Sci Data"},{"key":"1970_CR31","first-page":"2010","volume":"20252009","author":"Y Liu","year":"2025","unstructured":"Liu Y, Wang X, Zhang H, Yang R, Feng Y, Feng M, Yang T, Li Y, Qian S, Zhao C (2025) Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits. bioRxiv 20252009:2010\u2013675315","journal-title":"bioRxiv"},{"issue":"1","key":"1970_CR32","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/s41467-018-08260-0","volume":"10","author":"WY Low","year":"2019","unstructured":"Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun 10(1):260","journal-title":"Nat Commun"},{"issue":"5","key":"1970_CR33","first-page":"743","volume":"33","author":"H Mao","year":"2017","unstructured":"Mao H, Wang H (2017) SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets. Bioinf (Oxford England) 33(5):743\u2013745","journal-title":"Bioinf (Oxford England)"},{"key":"1970_CR34","doi-asserted-by":"crossref","unstructured":"Martchenko D, Chikhi R, Shafer ABA (2020) Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments. G3 Genes|Genomes|Genetics 10(2):437\u2013442","DOI":"10.1534\/g3.119.400747"},{"issue":"D1","key":"1970_CR35","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","volume":"49","author":"J Mistry","year":"2021","unstructured":"Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer EL, Tosatto SC, Paladin L, Raj S, Richardson LJ (2021) Pfam: The protein families database in 2021. Nucleic Acids Res 49(D1):D412\u2013D419","journal-title":"Nucleic Acids Res"},{"key":"1970_CR36","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.gde.2016.01.001","volume":"37","author":"P Mita","year":"2016","unstructured":"Mita P, Boeke JD (2016) How retrotransposons shape genome regulation. Curr Opin Genet Dev 37:90\u2013100","journal-title":"Curr Opin Genet Dev"},{"key":"1970_CR37","doi-asserted-by":"crossref","unstructured":"Quinlan AR (2014) BEDTools: the Swiss-army tool for genome feature analysis. Current protocols in bioinformatics 47(1):11.12. 11-11.12. 34","DOI":"10.1002\/0471250953.bi1112s47"},{"issue":"3","key":"1970_CR38","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1242\/dev.087585","volume":"140","author":"HM Rowe","year":"2013","unstructured":"Rowe HM, Friedli M, Offner S, Verp S, Mesnard D, Marquis J, Aktas T, Trono D (2013) De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs\/KAP1 and ESET. Development 140(3):519\u2013529","journal-title":"Development"},{"issue":"7440","key":"1970_CR39","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/nature11968","volume":"495","author":"RJ Schmitz","year":"2013","unstructured":"Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ (2013) Patterns of population epigenomic diversity. Nature 495(7440):193\u2013198","journal-title":"Nature"},{"key":"1970_CR40","doi-asserted-by":"publisher","unstructured":"Sharp JM, DeMartini JC (2003) Natural history of JSRV in sheep. In: Fan H (ed) Jaagsiekte sheep retrovirus and lung cancer. Springer, Berlin Heidelberg, pp 55\u201379. https:\/\/doi.org\/10.1007\/978-3-642-55638-8_3","DOI":"10.1007\/978-3-642-55638-8_3"},{"issue":"9","key":"1970_CR41","doi-asserted-by":"publisher","first-page":"e55101","DOI":"10.15252\/embr.202255101","volume":"23","author":"M Sorek","year":"2022","unstructured":"Sorek M, Meshorer E, Schlesinger S (2022) Impaired activation of transposable elements in SARS-CoV-2 infection. EMBO Rep 23(9):e55101","journal-title":"EMBO Rep"},{"issue":"12","key":"1970_CR42","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1101\/gr.168872.113","volume":"24","author":"V Sundaram","year":"2014","unstructured":"Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T (2014) Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res 24(12):1963\u20131976","journal-title":"Genome Res"},{"issue":"8","key":"1970_CR43","doi-asserted-by":"publisher","first-page":"1330","DOI":"10.1093\/gbe\/evaa124","volume":"12","author":"M Upadhyay","year":"2020","unstructured":"Upadhyay M, Hauser A, Kunz E, Krebs S, Blum H, Dotsev A, Okhlopkov I, Bagirov V, Brem G, Zinovieva N, Medugorac I (2020) The First Draft Genome Assembly of Snow Sheep (Ovis nivicola). Genome Biol Evol 12(8):1330\u20131336","journal-title":"Genome Biol Evol"},{"issue":"D1","key":"1970_CR44","doi-asserted-by":"publisher","first-page":"D83","DOI":"10.1093\/nar\/gks1263","volume":"41","author":"NS Vassetzky","year":"2013","unstructured":"Vassetzky NS, Kramerov DA (2013) SINEBase: a database and tool for SINE analysis. Nucleic Acids Res 41(D1):D83\u2013D89","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"1970_CR46","doi-asserted-by":"publisher","first-page":"5517","DOI":"10.3168\/jds.2022-22757","volume":"106","author":"M Wang","year":"2023","unstructured":"Wang M, Bissonnette N, Laterri\u00e8re M, Dudemaine P-L, Gagn\u00e9 D, Roy J-P, Sirard M-A, Ibeagha-Awemu (2023a) Gene co-expression in response to Staphylococcus aureus infection reveals networks of genes with specific functions during bovine subclinical mastitis. J Dairy Sci 106(8):5517\u20135536","journal-title":"J Dairy Sci"},{"key":"1970_CR48","doi-asserted-by":"crossref","unstructured":"Wang M, Bissonnette N, Laterri\u00e8re M, Gagn\u00e9 D, Dudemaine P-L, Roy J-P, Sirard M-A (2023b) and E. M. Ibeagha-Awemu. Genome-wide DNA methylation and transcriptome integration associates DNA methylation changes with bovine subclinical mastitis caused by Staphylococcus chromogenes. Int J Mol Sci 24(12):10369","DOI":"10.3390\/ijms241210369"},{"issue":"1","key":"1970_CR47","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1186\/s12915-024-01843-y","volume":"22","author":"M Wang","year":"2024","unstructured":"Wang M, Bissonnette N, Laterri\u00e8re M, Dudemaine P-L, Gagn\u00e9 D, Roy J-P, Sirard M-A, Ibeagha-Awemu EM (2024) DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits. BMC Biol 22(1):65","journal-title":"BMC Biol"},{"issue":"7","key":"1970_CR45","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1101\/gr.280357.124","volume":"35","author":"L Wang","year":"2025","unstructured":"Wang L, Taylor T, Rathnakumar K, Khyzha N, Liang M, Alizada A, Campitelli LF, Pour SE, Patel ZM, Antounians L, Tobias IC, Hou H, Hughes TR, Roy S, Mitchell JA, Fish JE, Wilson MD (2025) Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding. Genome Res 35(7):1544\u20131559","journal-title":"Genome Res"},{"issue":"9","key":"1970_CR49","doi-asserted-by":"publisher","first-page":"3117","DOI":"10.1105\/tpc.111.088682","volume":"23","author":"T Wenke","year":"2011","unstructured":"Wenke T, D\u00f6bel T, S\u00f6rensen TR, Junghans H, Weisshaar B, Schmidt T (2011) Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. Plant Cell 23(9):3117\u20133128","journal-title":"Plant Cell"},{"issue":"8","key":"1970_CR50","doi-asserted-by":"publisher","first-page":"evab168","DOI":"10.1093\/gbe\/evab168","volume":"13","author":"N Yang","year":"2021","unstructured":"Yang N, Zhao B, Chen Y, D\u2019Alessandro E, Chen C, Ji T, Wu X, Song C (2021) Distinct retrotransposon evolution profile in the genome of rabbit (Oryctolagus cuniculus). Genome biology Evol 13(8):evab168","journal-title":"Genome biology Evol"},{"issue":"8","key":"1970_CR51","doi-asserted-by":"publisher","first-page":"2081","DOI":"10.1016\/j.cell.2025.02.006","volume":"188","author":"T Yu","year":"2025","unstructured":"Yu T, Blyton MB, Abajorga M, Koppetsch BS, Ho S, Xu B, Hu Z, Luban J, Chappell K, Weng Z, Theurkauf WE (2025) Evolution of KoRV-A transcriptional silencing in wild koalas. Cell 188(8):2081\u20132093","journal-title":"Cell"},{"key":"1970_CR52","doi-asserted-by":"publisher","unstructured":"Zheng Y, Yang N, Chen C, Zong W, Chen H, Shi S, Wang X, Murani E, Reyer H, Gao B (2025) TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs. bioRxiv:2025.2005. 2021.653756. https:\/\/doi.org\/10.1101\/2025.05.21.653756","DOI":"10.1101\/2025.05.21.653756"},{"issue":"4","key":"1970_CR53","doi-asserted-by":"publisher","first-page":"R42","DOI":"10.1186\/gb-2009-10-4-r42","volume":"10","author":"AV Zimin","year":"2009","unstructured":"Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Mar\u00e7ais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10(4):R42","journal-title":"Genome Biol"}],"container-title":["Functional &amp; Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-01970-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-026-01970-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-01970-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T06:45:20Z","timestamp":1789541120000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10142-026-01970-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":53,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["1970"],"URL":"https:\/\/doi.org\/10.1007\/s10142-026-01970-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-9590742\/v1","asserted-by":"object"}]},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]},"assertion":[{"value":"2 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 June 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 June 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 September 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"266"}}