{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T03:34:10Z","timestamp":1793763250612,"version":"4.6.1"},"reference-count":102,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100007797","name":"University of Helsinki","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007797","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Sexual maturation is a key developmental process important for reproductive success. Understanding the molecular mechanisms behind variation in sexual maturation can provide insights into reproductive biology and how life history variation is encoded in the genome. Atlantic salmon (\n                      <jats:italic>Salmo salar<\/jats:italic>\n                      ) has become an excellent sexual maturation research model due to its diversity of life history strategies and its ecological and economic importance.\u00a0A major challenge has been the lack of a comprehensive transcriptional investigation of reproductive tissues that captures the dynamic transcriptional changes across individuals, tissues, and developmental stages. Long non-coding RNAs (lncRNAs) also play crucial roles in maturation, yet their functions in salmon maturation remain underexplored.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In this study, we sequenced 98 transcriptomes and found substantial transcriptomic complexity in the gonad and pituitary tissues of Atlantic salmon. We identified transcripts corresponding to 2,364 putative newly characterized protein-coding genes and 4,421 putative long intergenic non-coding RNAs (lincRNAs), many with tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules, linked to GO terms including Wnt signaling in immature testis, lipid metabolism, and cilia assembly in mature testis, ribosome biogenesis and DNA repair in the ovary, and hormone activity in pituitary. We identified new copies of known genes, such as\n                      <jats:italic>gh1<\/jats:italic>\n                      ,\n                      <jats:italic>pou3f2<\/jats:italic>\n                      , and\n                      <jats:italic>ier5<\/jats:italic>\n                      associated with the regulation of gonadal and pituitary functions. Some lncRNAs and their nearest genes showed correlated expression within modules, suggesting potential regulatory roles. Candidate lincRNAs indicated cis-acting regulatory potential on genes like\n                      <jats:italic>tnfrsf11b<\/jats:italic>\n                      and\n                      <jats:italic>fgl1<\/jats:italic>\n                      , which are implicated in immune privilege during gonadal development and sperm quality control.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our study provides a comprehensive transcriptomic analysis of Atlantic salmon gonad and pituitary tissues, significantly improving the functional annotation of the Atlantic salmon genome. These findings reveal key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in reproductive biology and maturation age variation, advancing our understanding of the molecular mechanisms governing sexual maturation. They further unlock future gene expression analyses and regulatory network reconstruction for dissecting the roles of lncRNAs in Atlantic salmon life history variation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-025-11954-7","type":"journal-article","created":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T08:59:00Z","timestamp":1758877140000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["A comprehensive analysis of Atlantic salmon gonad and pituitary transcriptomes identifies novel players in sexual maturation"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1820-7424","authenticated-orcid":false,"given":"Xin-Di","family":"Huang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9540-6518","authenticated-orcid":false,"given":"Morgane","family":"Frapin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6528-1187","authenticated-orcid":false,"given":"Ehsan Pashay","family":"Ahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3687-8435","authenticated-orcid":false,"given":"Craig Robert","family":"Primmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1701-6124","authenticated-orcid":false,"given":"Jukka-Pekka","family":"Verta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,9,26]]},"reference":[{"key":"11954_CR1","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s11160-021-09656-w","volume":"31","author":"KB Mobley","year":"2021","unstructured":"Mobley KB, Aykanat T, Czorlich Y, House A, Kurko J, Miettinen A, et al. Maturation in Atlantic salmon (Salmo salar, Salmonidae): a synthesis of ecological, genetic, and molecular processes. Rev Fish Biol Fish. 2021;31:523\u201371.","journal-title":"Rev Fish Biol Fish"},{"key":"11954_CR2","volume-title":"The evolution of life histories","author":"SC Stearns","year":"1992","unstructured":"Stearns SC. The evolution of life histories. New York: Oxford University Press; 1992."},{"key":"11954_CR3","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1890\/0012-9658(2001)082[0784:AASAFR]2.0.CO;2","volume":"82","author":"JX He","year":"2001","unstructured":"He JX, Stewart DJ. Age and size at first reproduction of fishes: predictive models based only on growth trajectories. Ecology. 2001;82:784\u201391.","journal-title":"Ecology"},{"key":"11954_CR4","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.1038\/s41559-019-0938-7","volume":"3","author":"K Healy","year":"2019","unstructured":"Healy K, Ezard THG, Jones OR, Salguero-G\u00f3mez R, Buckley YM. Animal life history is shaped by the pace of life and the distribution of age-specific mortality and reproduction. Nat Ecol Evol. 2019;3:1217\u201324.","journal-title":"Nat Ecol Evol"},{"key":"11954_CR5","doi-asserted-by":"publisher","first-page":"259","DOI":"10.2307\/2389364","volume":"3","author":"SC Stearns","year":"1989","unstructured":"Stearns SC. Trade-offs in life-history evolution. Funct Ecol. 1989;3:259\u201368.","journal-title":"Funct Ecol"},{"key":"11954_CR6","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1126\/science.aao6868","volume":"360","author":"DR Barneche","year":"2018","unstructured":"Barneche DR, Robertson DR, White CR, Marshall DJ. Fish reproductive-energy output increases disproportionately with body size. Science. 2018;360:642\u20135.","journal-title":"Science"},{"key":"11954_CR7","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1139\/cjfas-2017-0343","volume":"76","author":"J Erkinaro","year":"2019","unstructured":"Erkinaro J, Czorlich Y, Orell P, Kuusela J, Falkeg\u00e5rd M, L\u00e4nsman M, et al. Life history variation across four decades in a diverse population complex of Atlantic salmon in a large subarctic river. Can J Fish Aquat Sci. 2019;76:42\u201355.","journal-title":"Can J Fish Aquat Sci"},{"key":"11954_CR8","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1111\/jwas.12342","volume":"47","author":"C Good","year":"2016","unstructured":"Good C, Davidson J. A review of factors influencing maturation of Atlantic salmon, Salmo salar, with focus on water recirculation aquaculture system environments. J World Aquac Soc. 2016;47:605\u201332.","journal-title":"J World Aquac Soc"},{"key":"11954_CR9","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1080\/10454438.2016.1212756","volume":"28","author":"M Iversen","year":"2016","unstructured":"Iversen M, Myhr AI, Wargelius A. Approaches for delaying sexual maturation in salmon and their possible ecological and ethical implications. J Appl Aquac. 2016;28:330\u201369.","journal-title":"J Appl Aquac"},{"key":"11954_CR10","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/j.ygcen.2009.05.004","volume":"165","author":"GL Taranger","year":"2010","unstructured":"Taranger GL, Carrillo M, Schulz RW, Fontaine P, Zanuy S, Felip A, et al. Control of puberty in farmed fish. Gen Comp Endocrinol. 2010;165:483\u2013515.","journal-title":"Gen Comp Endocrinol"},{"key":"11954_CR11","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.yhbeh.2013.02.012","volume":"64","author":"BJ Ellis","year":"2013","unstructured":"Ellis BJ. The hypothalamic\u2013pituitary\u2013gonadal axis: a switch-controlled, condition-sensitive system in the regulation of life history strategies. Horm Behav. 2013;64:215\u201325.","journal-title":"Horm Behav"},{"key":"11954_CR12","doi-asserted-by":"publisher","first-page":"114055","DOI":"10.1016\/j.ygcen.2022.114055","volume":"325","author":"EP Ahi","year":"2022","unstructured":"Ahi EP, Sinclair-Waters M, Moustakas-Verho J, Jansouz S, Primmer CR. Strong regulatory effects of vgll3 genotype on reproductive axis gene expression in juvenile male Atlantic salmon. Gen Comp Endocrinol. 2022;325:114055.","journal-title":"Gen Comp Endocrinol"},{"key":"11954_CR13","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1186\/s12864-022-08514-8","volume":"23","author":"AR Mohamed","year":"2022","unstructured":"Mohamed AR, Naval-Sanchez M, Menzies M, Evans B, King H, Reverter A, et al. Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation. BMC Genomics. 2022;23:413.","journal-title":"BMC Genomics"},{"key":"11954_CR14","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, Stamatoyannopoulos JA, Dutta A, Guig\u00f3 R, Gingeras TR, Margulies EH, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799\u2013816.","journal-title":"Nature"},{"key":"11954_CR15","doi-asserted-by":"publisher","first-page":"e1004351","DOI":"10.1371\/journal.pgen.1004351","volume":"10","author":"AF Palazzo","year":"2014","unstructured":"Palazzo AF, Gregory TR. The case for junk DNA. PLoS Genet. 2014;10:e1004351.","journal-title":"PLoS Genet"},{"key":"11954_CR16","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/j.cell.2009.02.006","volume":"136","author":"CP Ponting","year":"2009","unstructured":"Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136:629\u201341.","journal-title":"Cell"},{"key":"11954_CR17","doi-asserted-by":"crossref","unstructured":"Solomon CU, McVey DG, Andreadi C, Gong P, Turner L, Khemiri S, et al. Identification and Characterization of novel long non-coding RNAs in vascular smooth cells. 2023.","DOI":"10.1101\/2023.01.06.523019"},{"key":"11954_CR18","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.tplants.2017.12.009","volume":"23","author":"AA Golicz","year":"2018","unstructured":"Golicz AA, Bhalla PL, Singh MB. LncRNAs in plant and animal sexual reproduction. Trends Plant Sci. 2018;23:195\u2013205.","journal-title":"Trends Plant Sci"},{"key":"11954_CR19","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1186\/s12864-017-4205-5","volume":"18","author":"KO Skaftnesmo","year":"2017","unstructured":"Skaftnesmo KO, Edvardsen RB, Furmanek T, Crespo D, Andersson E, Kleppe L, et al. Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon. BMC Genomics. 2017;18:801.","journal-title":"BMC Genomics"},{"key":"11954_CR20","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1007\/s10126-021-10024-9","volume":"23","author":"V Valenzuela-Mu\u00f1oz","year":"2021","unstructured":"Valenzuela-Mu\u00f1oz V, V\u00e1ldes JA, Gallardo-Esc\u00e1rate C. Transcriptome profiling of long non-coding RNAs during the Atlantic Salmon smoltification process. Mar Biotechnol. 2021;23:308\u201320.","journal-title":"Mar Biotechnol"},{"key":"11954_CR21","doi-asserted-by":"publisher","first-page":"22698","DOI":"10.1038\/srep22698","volume":"6","author":"S Bolta\u00f1a","year":"2016","unstructured":"Bolta\u00f1a S, Valenzuela-Miranda D, Aguilar A, Mackenzie S, Gallardo-Esc\u00e1rate C. Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-infected Atlantic salmon (Salmo salar). Sci Rep. 2016;6:22698.","journal-title":"Sci Rep"},{"key":"11954_CR22","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1186\/s13059-019-1710-7","volume":"20","author":"A Morillon","year":"2019","unstructured":"Morillon A, Gautheret D. Bridging the gap between reference and real transcriptomes. Genome Biol. 2019;20:112.","journal-title":"Genome Biol"},{"key":"11954_CR23","doi-asserted-by":"publisher","DOI":"10.1530\/REP-19-0092","author":"J Gamble","year":"2020","unstructured":"Gamble J, Chick J, Seltzer K, Graber JH, Gygi S, Braun RE, et al. An expanded mouse testis transcriptome and mass spectrometry defines novel proteins. Reproduction. 2020. https:\/\/doi.org\/10.1530\/REP-19-0092.","journal-title":"Reproduction"},{"key":"11954_CR24","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1101\/gr.101386.109","volume":"20","author":"H Kaessmann","year":"2010","unstructured":"Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 2010;20:1313\u201326.","journal-title":"Genome Res"},{"key":"11954_CR25","doi-asserted-by":"publisher","first-page":"1912","DOI":"10.1038\/s41598-018-20308-1","volume":"8","author":"E Kj\u00e6rner-Semb","year":"2018","unstructured":"Kj\u00e6rner-Semb E, Ayllon F, Kleppe L, S\u00f8rhus E, Skaftnesmo K, Furmanek T, et al. Vgll3 and the Hippo pathway are regulated in Sertoli cells upon entry and during puberty in Atlantic salmon testis. Sci Rep. 2018;8:1912.","journal-title":"Sci Rep"},{"key":"11954_CR26","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s12864-020-6513-4","volume":"21","author":"L Kleppe","year":"2020","unstructured":"Kleppe L, Edvardsen RB, Furmanek T, Andersson E, Skaftnesmo KO, Thyri Segafredo F, et al. Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon. BMC Genomics. 2020;21:99.","journal-title":"BMC Genomics"},{"key":"11954_CR27","doi-asserted-by":"publisher","first-page":"e2402386121","DOI":"10.1073\/pnas.2402386121","volume":"121","author":"JP Verta","year":"2024","unstructured":"Verta JP, Moustakas-Verho JE, Donner I, Frapin M, Ruokolainen A, Debes PV, et al. A complex mechanism translating variation of a simple genetic architecture into alternative life histories. Proc Natl Acad Sci U S A. 2024;121:e2402386121.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"11954_CR28","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nrg3068","volume":"12","author":"JA Martin","year":"2011","unstructured":"Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011;12:671\u201382.","journal-title":"Nat Rev Genet"},{"key":"11954_CR29","doi-asserted-by":"publisher","first-page":"740151","DOI":"10.1016\/j.aquaculture.2023.740151","volume":"579","author":"EP Ahi","year":"2024","unstructured":"Ahi EP, Frapin M, Hukkanen M, Primmer CR. Hypothalamic expression analysis of m6A RNA methylation associated genes suggests a potential role of epitranscriptomics in sexual maturation of Atlantic salmon. Aquaculture. 2024;579:740151.","journal-title":"Aquaculture"},{"key":"11954_CR30","doi-asserted-by":"publisher","first-page":"coac086","DOI":"10.1093\/conphys\/coac086","volume":"11","author":"ER \u00c5sheim","year":"2023","unstructured":"\u00c5sheim ER, Debes PV, House A, Liljestr\u00f6m P, Niemel\u00e4 PT, Siren JP, et al. Atlantic salmon (Salmo salar) age at maturity is strongly affected by temperature, population and age-at-maturity genotype. Conserv Physiol. 2023;11:coac086.","journal-title":"Conserv Physiol"},{"key":"11954_CR31","doi-asserted-by":"publisher","first-page":"e17735","DOI":"10.1111\/mec.17735","volume":"34","author":"KS Maamela","year":"2025","unstructured":"Maamela KS, \u00c5sheim ER, O\u2019Sullivan RJ, Debes PV, House AH, Liljestr\u00f6m P, et al. Food quality and life-history genotype influence maturation and reproductive traits in female Atlantic salmon. Mol Ecol. 2025;34:e17735.","journal-title":"Mol Ecol"},{"key":"11954_CR32","unstructured":"BioanalyzeR. GitHub. https:\/\/github.com\/jwfoley\/bioanalyzeR."},{"key":"11954_CR33","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884\u201390.","journal-title":"Bioinformatics"},{"key":"11954_CR34","doi-asserted-by":"publisher","first-page":"D933","DOI":"10.1093\/nar\/gkac958","volume":"51","author":"FJ Martin","year":"2023","unstructured":"Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, et al. Ensembl 2023. Nucleic Acids Res. 2023;51:D933\u201341.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR35","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinforma Oxf Engl. 2013;29:15\u201321.","journal-title":"Bioinforma Oxf Engl"},{"key":"11954_CR36","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1038\/nprot.2016.095","volume":"11","author":"M Pertea","year":"2016","unstructured":"Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11:1650\u201367.","journal-title":"Nat Protoc"},{"key":"11954_CR37","doi-asserted-by":"publisher","first-page":"ISCB Comm J-304","DOI":"10.12688\/f1000research.23297.1","volume":"9","author":"G Pertea","year":"2020","unstructured":"Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. . F1000Research. 2020;9:ISCB Comm J-304.","journal-title":". F1000Research"},{"key":"11954_CR38","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1093\/bfgp\/elab045","volume":"21","author":"T Ammun\u00e9t","year":"2022","unstructured":"Ammun\u00e9t T, Wang N, Khan S, Elo LL. Deep learning tools are top performers in long non-coding RNA prediction. Brief Funct Genomics. 2022;21:230\u201341.","journal-title":"Brief Funct Genomics"},{"key":"11954_CR39","first-page":"e57","volume":"45","author":"V Wucher","year":"2017","unstructured":"Wucher V, Legeai F, H\u00e9dan B, Rizk G, Lagoutte L, Leeb T, et al. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res. 2017;45:e57.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR40","unstructured":"TransDecoder. GitHub. https:\/\/github.com\/TransDecoder\/TransDecoder\/wiki\/Home."},{"key":"11954_CR41","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 ELL, et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412\u20139.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR42","unstructured":"HMMER. http:\/\/hmmer.org\/."},{"key":"11954_CR43","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38:5825\u20139.","journal-title":"Mol Biol Evol"},{"key":"11954_CR44","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","volume":"47","author":"J Huerta-Cepas","year":"2019","unstructured":"Huerta-Cepas J, Szklarczyk D, Heller D, Hern\u00e1ndez-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309-14.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR45","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson JT, Thorvaldsd\u00f3ttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24\u20136.","journal-title":"Nat Biotechnol"},{"key":"11954_CR46","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923\u201330.","journal-title":"Bioinformatics"},{"key":"11954_CR47","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.","journal-title":"Genome Biol"},{"key":"11954_CR48","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57:289\u2013300.","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"11954_CR49","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","volume":"16","author":"C Chen","year":"2023","unstructured":"Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, et al. TBtools-II: A \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining. Mol Plant. 2023;16:1733\u201342.","journal-title":"Mol Plant"},{"key":"11954_CR50","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1093\/bioinformatics\/bti042","volume":"21","author":"I Yanai","year":"2005","unstructured":"Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21:650\u20139.","journal-title":"Bioinformatics"},{"key":"11954_CR51","first-page":"205","volume":"18","author":"N Kryuchkova-Mostacci","year":"2017","unstructured":"Kryuchkova-Mostacci N, Robinson-Rechavi M. A benchmark of gene expression tissue-specificity metrics. Brief Bioinform. 2017;18:205\u201314.","journal-title":"Brief Bioinform"},{"key":"11954_CR52","doi-asserted-by":"publisher","first-page":"3864","DOI":"10.1093\/nar\/gkq1348","volume":"39","author":"Q Liao","year":"2011","unstructured":"Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, et al. Large-scale prediction of long non-coding RNA functions in a coding\u2013non-coding gene co-expression network. Nucleic Acids Res. 2011;39:3864\u201378.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR53","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1007\/s10126-016-9689-5","volume":"18","author":"J Wang","year":"2016","unstructured":"Wang J, Fu L, Koganti PP, Wang L, Hand JM, Ma H, et al. Identification and functional prediction of large intergenic noncoding RNAs (lincRNAs) in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol. 2016;18:271\u201382.","journal-title":"Mar Biotechnol"},{"key":"11954_CR54","doi-asserted-by":"crossref","unstructured":"Dai R, Xia Y, Liu C, Chen C. csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations. 2018;:288225.","DOI":"10.1101\/288225"},{"key":"11954_CR55","doi-asserted-by":"publisher","first-page":"W193","DOI":"10.1093\/nar\/gkm226","volume":"35 Web Server i","author":"J Reimand","year":"2007","unstructured":"Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler\u2014a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007;35 Web Server issue:W193-200.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR56","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16:284\u20137.","journal-title":"OMICS"},{"key":"11954_CR57","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1002\/path.5405","volume":"250","author":"I Tsagakis","year":"2020","unstructured":"Tsagakis I, Douka K, Birds I, Aspden JL. Long non-coding RNAs in development and disease: conservation to mechanisms. J Pathol. 2020;250:480.","journal-title":"J Pathol"},{"key":"11954_CR58","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1111\/age.12539","volume":"48","author":"XF Liu","year":"2017","unstructured":"Liu XF, Ding XB, Li X, Jin CF, Yue YW, Li GP, et al. An atlas and analysis of bovine skeletal muscle long noncoding RNAs. Anim Genet. 2017;48:278\u201386.","journal-title":"Anim Genet"},{"key":"11954_CR59","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1007\/s10142-016-0524-x","volume":"17","author":"E Deniz","year":"2017","unstructured":"Deniz E, Erman B. Long noncoding RNA (lincRNA), a new paradigm in gene expression control. Funct Integr Genomics. 2017;17:135\u201343.","journal-title":"Funct Integr Genomics"},{"key":"11954_CR60","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.11781","volume":"9","author":"S Cervantes","year":"2021","unstructured":"Cervantes S, Vuosku J, Pyh\u00e4j\u00e4rvi T. Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris. PeerJ. 2021;9: e11781.","journal-title":"PeerJ"},{"key":"11954_CR61","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s13040-022-00315-9","volume":"15","author":"HB L\u00fcleci","year":"2022","unstructured":"L\u00fcleci HB, Y\u0131lmaz A. Robust and rigorous identification of tissue-specific genes by statistically extending tau score. BioData Min. 2022;15:31.","journal-title":"BioData Min"},{"key":"11954_CR62","doi-asserted-by":"publisher","first-page":"685341","DOI":"10.3389\/fgene.2021.685341","volume":"12","author":"PK Chitneedi","year":"2021","unstructured":"Chitneedi PK, Weikard R, Arranz JJ, Mart\u00ednez-Valladares M, Kuehn C, Guti\u00e9rrez-Gil B. Identification of regulatory functions of LncRNAs associated with T. circumcincta infection in adult sheep. Front Genet. 2021;12:685341.","journal-title":"Front Genet"},{"key":"11954_CR63","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1471-2105-9-559","volume":"9","author":"P Langfelder","year":"2008","unstructured":"Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.","journal-title":"BMC Bioinformatics"},{"key":"11954_CR64","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1186\/s12864-020-06805-6","volume":"21","author":"Z Yang","year":"2020","unstructured":"Yang Z, Dai Z, Chen X, Xie D, Tang Q, Cheng C, et al. Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.). BMC Genomics. 2020;21:406.","journal-title":"BMC Genomics"},{"key":"11954_CR65","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1038\/s41580-023-00694-9","volume":"25","author":"J Ferrer","year":"2024","unstructured":"Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol. 2024;25:396\u2013415.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"11954_CR66","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/1741-7007-11-59","volume":"11","author":"AE Kornienko","year":"2013","unstructured":"Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol. 2013;11:59.","journal-title":"BMC Biol"},{"key":"11954_CR67","doi-asserted-by":"publisher","first-page":"1845","DOI":"10.1126\/science.1162228","volume":"322","author":"LJ Core","year":"2008","unstructured":"Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322:1845\u20138.","journal-title":"Science"},{"key":"11954_CR68","doi-asserted-by":"publisher","first-page":"2876","DOI":"10.1073\/pnas.1221904110","volume":"110","author":"AA Sigova","year":"2013","unstructured":"Sigova AA, Mullen AC, Molinie B, Gupta S, Orlando DA, Guenther MG, et al. Divergent transcription of long noncoding RNA\/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A. 2013;110:2876\u201381.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"11954_CR69","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1186\/s13059-021-02350-x","volume":"22","author":"F Agostini","year":"2021","unstructured":"Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol. 2021;22:136.","journal-title":"Genome Biol"},{"key":"11954_CR70","doi-asserted-by":"publisher","first-page":"e1000371","DOI":"10.1371\/journal.pbio.1000371","volume":"8","author":"H van Bakel","year":"2010","unstructured":"van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most \u201cDark Matter\u201d transcripts are associated with known genes. PLoS Biol. 2010;8:e1000371.","journal-title":"PLoS Biol"},{"key":"11954_CR71","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1038\/nature20149","volume":"539","author":"JM Engreitz","year":"2016","unstructured":"Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature. 2016;539:452\u20135.","journal-title":"Nature"},{"key":"11954_CR72","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1038\/s41467-024-45028-1","volume":"15","author":"J Peng","year":"2024","unstructured":"Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nat Commun. 2024;15:810.","journal-title":"Nat Commun"},{"key":"11954_CR73","doi-asserted-by":"publisher","first-page":"9935","DOI":"10.1073\/pnas.0509809103","volume":"103","author":"MT Levine","year":"2006","unstructured":"Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci. 2006;103:9935\u20139.","journal-title":"Proc Natl Acad Sci"},{"key":"11954_CR74","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1016\/j.tcb.2024.02.010","volume":"34","author":"C Alfonso-Gonzalez","year":"2024","unstructured":"Alfonso-Gonzalez C, Hilgers V. (Alternative) transcription start sites as regulators of RNA processing. Trends Cell Biol. 2024;34:1018\u201328.","journal-title":"Trends Cell Biol"},{"key":"11954_CR75","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1093\/nar\/gkx1165","volume":"46","author":"A Reyes","year":"2018","unstructured":"Reyes A, Huber W. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res. 2018;46:582\u201392.","journal-title":"Nucleic Acids Res"},{"key":"11954_CR76","doi-asserted-by":"publisher","first-page":"614","DOI":"10.3390\/genes12050614","volume":"12","author":"X Chen","year":"2021","unstructured":"Chen X, Sun Z. Novel lincRNA discovery and tissue-specific gene expression across 30 normal human tissues. Genes. 2021;12:614.","journal-title":"Genes"},{"key":"11954_CR77","doi-asserted-by":"publisher","first-page":"2179","DOI":"10.1016\/j.celrep.2013.05.031","volume":"3","author":"M Soumillon","year":"2013","unstructured":"Soumillon M, Necsulea A, Weier M, Brawand D, Zhang X, Gu H, et al. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell Rep. 2013;3:2179\u201390.","journal-title":"Cell Rep"},{"key":"11954_CR78","doi-asserted-by":"crossref","unstructured":"Yang RY, Quan J, Sodaei R, Aguet F, Segr\u00e8 AV, Allen JA, et al. A systematic survey of human tissue-specific gene expression and splicing reveals new opportunities for therapeutic target identification and evaluation. 2018.","DOI":"10.1101\/311563"},{"key":"11954_CR79","doi-asserted-by":"publisher","first-page":"e170","DOI":"10.1371\/journal.pbio.0030170","volume":"3","author":"R Nielsen","year":"2005","unstructured":"Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 2005;3:e170.","journal-title":"PLoS Biol"},{"key":"11954_CR80","doi-asserted-by":"publisher","first-page":"8315","DOI":"10.1073\/pnas.0709854105","volume":"105","author":"DS Johnston","year":"2008","unstructured":"Johnston DS, Wright WW, DiCandeloro P, Wilson E, Kopf GS, Jelinsky SA. Stage-specific gene expression is a fundamental characteristic of rat spermatogenic cells and Sertoli cells. Proc Natl Acad Sci U S A. 2008;105:8315\u201320.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"11954_CR81","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.bbagrm.2013.08.004","volume":"1839","author":"C Rathke","year":"2014","unstructured":"Rathke C, Baarends WM, Awe S, Renkawitz-Pohl R. Chromatin dynamics during spermiogenesis. Biochim Biophys Acta BBA - Gene Regul Mech. 2014;1839:155\u201368.","journal-title":"Biochim Biophys Acta BBA - Gene Regul Mech"},{"key":"11954_CR82","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.cell.2019.12.015","volume":"180","author":"B Xia","year":"2020","unstructured":"Xia B, Yan Y, Baron M, Wagner F, Barkley D, Chiodin M, et al. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell. 2020;180:248-262.e21.","journal-title":"Cell"},{"key":"11954_CR83","doi-asserted-by":"publisher","first-page":"3225","DOI":"10.1093\/molbev\/msaa168","volume":"37","author":"H Liu","year":"2020","unstructured":"Liu H, Zhang J. Higher germline mutagenesis of genes with stronger testis expressions refutes the transcriptional scanning hypothesis. Mol Biol Evol. 2020;37:3225\u201331.","journal-title":"Mol Biol Evol"},{"key":"11954_CR84","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.gene.2015.04.066","volume":"565","author":"WL Dong","year":"2015","unstructured":"Dong WL, Tan FQ, Yang WX. Wnt signaling in testis development: unnecessary or essential? Gene. 2015;565:155\u201365.","journal-title":"Gene"},{"key":"11954_CR85","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1095\/biolreprod.112.105809","volume":"90","author":"GE Kerr","year":"2014","unstructured":"Kerr GE, Young JC, Horvay K, Abud HE, Loveland KL. Regulated Wnt\/beta-catenin signaling sustains adult spermatogenesis in mice. Biol Reprod. 2014;90:3.","journal-title":"Biol Reprod"},{"key":"11954_CR86","doi-asserted-by":"publisher","first-page":"1991","DOI":"10.1093\/humrep\/deaa150","volume":"35","author":"JC Young","year":"2020","unstructured":"Young JC, Kerr G, Micati D, Nielsen JE, Rajpert-De Meyts E, Abud HE, et al. Wnt signalling in the normal human adult testis and in male germ cell neoplasms. Hum Reprod. 2020;35:1991\u20132003.","journal-title":"Hum Reprod"},{"key":"11954_CR87","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1186\/s12864-019-5869-9","volume":"20","author":"D Crespo","year":"2019","unstructured":"Crespo D, Bogerd J, Sambroni E, LeGac F, Andersson E, Edvardsen RB, et al. The initiation of puberty in Atlantic salmon brings about large changes in testicular gene expression that are modulated by the energy status. BMC Genomics. 2019;20:475.","journal-title":"BMC Genomics"},{"key":"11954_CR88","doi-asserted-by":"publisher","first-page":"625","DOI":"10.2164\/jandrol.111.012989","volume":"32","author":"MP Hedger","year":"2011","unstructured":"Hedger MP. Immunophysiology and pathology of inflammation in the testis and epididymis. J Androl. 2011;32:625\u201340.","journal-title":"J Androl"},{"key":"11954_CR89","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/nature17164","volume":"533","author":"S Lien","year":"2016","unstructured":"Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533:200\u20135.","journal-title":"Nature"},{"key":"11954_CR90","doi-asserted-by":"publisher","first-page":"evab059","DOI":"10.1093\/gbe\/evab059","volume":"13","author":"JP Verta","year":"2021","unstructured":"Verta JP, Barton HJ, Pritchard V, Primmer CR. Genetic drift dominates genome-wide regulatory evolution following an ancient whole-genome duplication in Atlantic Salmon. Genome Biol Evol. 2021;13:evab059.","journal-title":"Genome Biol Evol"},{"key":"11954_CR91","doi-asserted-by":"publisher","first-page":"evac126","DOI":"10.1093\/gbe\/evac126","volume":"14","author":"A Luzuriaga-Neira","year":"2022","unstructured":"Luzuriaga-Neira A, Subramanian K, Alvarez-Ponce D. Functional compensation of mouse duplicates by their paralogs expressed in the same tissues. Genome Biol Evol. 2022;14:evac126.","journal-title":"Genome Biol Evol"},{"key":"11954_CR92","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1016\/j.cell.2013.02.012","volume":"152","author":"PJ Batista","year":"2013","unstructured":"Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013;152:1298\u2013307.","journal-title":"Cell"},{"key":"11954_CR93","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","volume":"24","author":"JS Mattick","year":"2023","unstructured":"Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen L-L, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023;24:430\u201347.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"11954_CR94","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1002\/mrd.22581","volume":"82","author":"DH Taylor","year":"2015","unstructured":"Taylor DH, Chu ET-J, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev. 2015;82:932\u201356.","journal-title":"Mol Reprod Dev"},{"key":"11954_CR95","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1038\/nsmb.2428","volume":"19","author":"S Guil","year":"2012","unstructured":"Guil S, Esteller M. Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol. 2012;19:1068\u201375.","journal-title":"Nat Struct Mol Biol"},{"key":"11954_CR96","doi-asserted-by":"publisher","first-page":"2450","DOI":"10.1038\/s41467-021-22734-8","volume":"12","author":"M Blomberg Jensen","year":"2021","unstructured":"Blomberg Jensen M, Andreassen CH, J\u00f8rgensen A, Nielsen JE, Juel Mortensen L, Boisen IM, et al. RANKL regulates male reproductive function. Nat Commun. 2021;12:2450.","journal-title":"Nat Commun"},{"key":"11954_CR97","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.1002\/mrd.23438","volume":"87","author":"SK Nagdas","year":"2020","unstructured":"Nagdas SK, Wallace S, Eaford D, Baker R, Carr K, Raychoudhuri SS. Fibrinogen-related protein, FGL2, of hamster cauda epididymal fluid: purification, kinetic analysis of its prothrombinase activity, and its role in segregation of nonviable spermatozoa. Mol Reprod Dev. 2020;87:1206\u201318.","journal-title":"Mol Reprod Dev"},{"key":"11954_CR98","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s12867-015-0051-7","volume":"16","author":"D Fietz","year":"2015","unstructured":"Fietz D, Markmann M, Lang D, Konrad L, Geyer J, Kliesch S, et al. Transfection of Sertoli cells with androgen receptor alters gene expression without androgen stimulation. BMC Mol Biol. 2015;16:23.","journal-title":"BMC Mol Biol"},{"key":"11954_CR99","doi-asserted-by":"publisher","first-page":"R16","DOI":"10.1186\/gb-2011-12-2-r16","volume":"12","author":"L Yang","year":"2011","unstructured":"Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 2011;12:R16.","journal-title":"Genome Biol"},{"key":"11954_CR100","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.biocel.2013.10.009","volume":"54","author":"Y Zhang","year":"2014","unstructured":"Zhang Y, Yang L, Chen L-L. Life without a tail: new formats of long noncoding RNAs. Int J Biochem Cell Biol. 2014;54:338\u201349.","journal-title":"Int J Biochem Cell Biol"},{"key":"11954_CR101","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1186\/s12864-015-1308-8","volume":"16","author":"S Zhao","year":"2015","unstructured":"Zhao S, Zhang B. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics. 2015;16:97.","journal-title":"BMC Genomics"},{"key":"11954_CR102","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nmeth.4078","volume":"14","author":"YS Niknafs","year":"2017","unstructured":"Niknafs YS, Pandian B, Iyer HK, Chinnaiyan AM, Iyer MK. TACO produces robust multi-sample transcriptome assemblies from RNA-seq. Nat Methods. 2017;14:68\u201370.","journal-title":"Nat Methods"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-025-11954-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-025-11954-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-025-11954-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T11:35:41Z","timestamp":1781609741000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12864-025-11954-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,26]]},"references-count":102,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["11954"],"URL":"https:\/\/doi.org\/10.1186\/s12864-025-11954-7","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,26]]},"assertion":[{"value":"20 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 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":"The rearing and sampling of Atlantic salmon were performed according to European animal welfare regulations and approved by the Finnish Project Authorization Board (permits ESAVI\/2778\/2018 and ESAVI\/4511\/2020).","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":"818"}}