{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T15:12:26Z","timestamp":1768921946058,"version":"3.49.0"},"reference-count":46,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T00:00:00Z","timestamp":1701216000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key R&amp;D Program of China","award":["2021YFD1200304"],"award-info":[{"award-number":["2021YFD1200304"]}]},{"name":"National Key R&amp;D Program of China","award":["31602165"],"award-info":[{"award-number":["31602165"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2021YFD1200304"],"award-info":[{"award-number":["2021YFD1200304"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31602165"],"award-info":[{"award-number":["31602165"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Brachymystax tsinlingensis Li is an endangered cold-water salmonid fish native to China. This study aimed to identify sex-related genes and biological pathways via gonadal transcriptome sequencing of B. tsinlingensis Li. A total of 167,904 unigenes were identified with an average length of 836 bp and an N50 of 1452 bp, of which 84,977 (50.61%) unigenes were successfully annotated in six major databases. Comparative transcriptome analysis identified 22,864 differentially expressed genes (DEGs), of which 17,231 were up-regulated (male-biased genes, mDEGs) and 5633 were down-regulated (female-biased genes, fDEGs). Several DEGs associated with gonadal development were found through Gene Ontology enrichment analysis, such as ccnb1, zp3, bmp15, dmrt1, and psmc3ip. Signaling pathways related to gonadal development were found to be enriched through analysis using the Kyoto Encyclopedia of Genes and Genomes Pathway database, such as genes involves in base excision repair, the notch signaling pathway, neuroactive ligand-receptor interaction, the VEGF signaling pathway, and the estrogen signaling pathway. In addition, mRNA expression levels of 19 DEGs were determined to validate the reliability of the transcriptomic data by quantitative real-time polymerase chain reaction. These results revealed genes and signaling pathways potentially involved in gonadal development in B. tsinlingensis Li and provided basic molecular data for future research on reproductive regulation and breeding of B. tsinlingensis Li.<\/jats:p>","DOI":"10.3390\/ani13233690","type":"journal-article","created":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T03:48:24Z","timestamp":1701229704000},"page":"3690","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Comparative Transcriptome Analysis Reveals Sexually Dimorphic Gene Expression in the Gonads of Brachymystax tsinlingensis Li"],"prefix":"10.3390","volume":"13","author":[{"given":"Ling","family":"Huang","sequence":"first","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan","family":"Ye","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huamei","family":"Yue","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqian","family":"Leng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Ruan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0018-1740","authenticated-orcid":false,"given":"Hao","family":"Du","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuangju","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinming","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,29]]},"reference":[{"key":"ref_1","first-page":"809","article-title":"The validity of species of Brachymystax tsinlingensis Li based on mitochondria control region and microsatellite","volume":"47","author":"Xiong","year":"2023","journal-title":"Acta Hydrobiol. Sin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/s11284-016-1418-z","article-title":"Effects of temperature acclimation on the critical thermal limits and swimming performance of Brachymystax lenok tsinlingensis: A threatened fish in Qinling Mountain region of China","volume":"32","author":"Xia","year":"2017","journal-title":"Ecol. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/s10641-008-9337-7","article-title":"Threatened fishes of the world: Brachymystax lenok tsinlingensis Li, 1966 (Salmonidae)","volume":"86","author":"Zhao","year":"2009","journal-title":"Environ. Biol. Fishes."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Li, P., Liu, Q., Li, J., Wang, F., Wen, S., and Li, N. (2021). Transcriptomic responses to heat stress in gill and liver of endangered Brachymystax lenok tsinlingensis. Comp. Biochem. Physiol. Part. D Genom. Proteom., 38.","DOI":"10.1016\/j.cbd.2021.100791"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1007\/s13258-020-00939-3","article-title":"De novo assembly and microsatellite marker development of the transcriptome of the endangered Brachymystax lenok tsinlingensis","volume":"42","author":"Wen","year":"2020","journal-title":"Genes. Genom."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1007\/s10126-022-10175-3","article-title":"Effect of astaxanthin on the antioxidant capacity and intestinal microbiota of tsinling lenok trout (Brachymystax lenok tsinlingensis)","volume":"24","author":"Ma","year":"2022","journal-title":"Mar. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.tice.2016.05.009","article-title":"Morphology and ultrastructure of Brachymystax lenok tsinlingensis spermatozoa by scanning and transmission electron microscopy","volume":"48","author":"Guo","year":"2016","journal-title":"Tissue Cell."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wang, Z., Sun, L., Guan, W., Zhou, C., Tang, B., Cheng, Y., Huang, J., and Xuan, F. (2018). De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II). BMC Genet., 19.","DOI":"10.1186\/s12863-017-0592-5"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Lin, X., Zhou, D., Zhang, X., Li, G., Zhang, Y., Huang, C., Zhang, Z., and Tian, C. (2021). A first insight into the gonad transcriptome of hong kong catfish (Clarias fuscus). Animals, 11.","DOI":"10.3390\/ani11041131"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1007\/s10126-022-10127-x","article-title":"Comprehensive transcriptome analysis of gonadal and somatic tissues for identification of sex-related genes in the largemouth bass Micropterus salmoides","volume":"24","author":"Guan","year":"2022","journal-title":"Mar. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Gou, P., Wang, Z., Yang, J., Wang, X., and Qiu, X. (2022). Comparative transcriptome analysis of differentially expressed genes in the testis and ovary of sea urchin (Strongylocentrotus intermedius). Fishes, 7.","DOI":"10.3390\/fishes7040152"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1530\/REP-20-0264","article-title":"FGF2\/FGRG signaling promotes cumulus-oocyte complex maturation in vitro","volume":"161","author":"Du","year":"2021","journal-title":"Reproduction"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1080\/15384101.2022.2074740","article-title":"Knockout of cyclin B1 in granulosa cells causes female subfertility","volume":"21","author":"Cheng","year":"2022","journal-title":"Cell Cycle"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"41272","DOI":"10.1038\/srep41272","article-title":"ZP3 is required for germinal vesicle breakdown in mouse oocyte meiosis","volume":"7","author":"Gao","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1242\/dev.009068","article-title":"Oocyte regulation of metabolic cooperativity between mouse cumulus cells and oocytes: BMP15 and GDF9 control cholesterol biosynthesis in cumulus cells","volume":"135","author":"Su","year":"2008","journal-title":"Development"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Dranow, D.B., Hu, K., Bird, A.M., Lawry, S.T., Adams, M.T., Sanchez, A., Amatruda, J.F., and Draper, B.W. (2016). Bmp15 is an oocyte-produced signal required for maintenance of the adult female sexual phenotype in zebrafish. PLoS Genet., 12.","DOI":"10.1371\/journal.pgen.1006323"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Huang, Y., Jiang, D., Li, M., Mustapha, U.F., Tian, C., Chen, H., Huang, Y., Deng, S., Wu, T., and Zhu, C. (2019). Genome survey of male and female spotted scat (Scatophagus argus). Animals, 9.","DOI":"10.3390\/ani9121117"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"11778","DOI":"10.1073\/pnas.182314699","article-title":"A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes","volume":"99","author":"Nanda","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1095\/biolreprod.106.058784","article-title":"Sex-specific differences in mouse DMRT1 expression are both cell type- and stage-dependent during gonad development","volume":"77","author":"Lei","year":"2007","journal-title":"Biol. Reprod."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1006\/dbio.1999.9461","article-title":"Expression of Dmrt1 in the genital ridge of mouse and chicken embryos suggests a role in vertebrate sexual development","volume":"215","author":"Raymond","year":"1999","journal-title":"Dev. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"619","DOI":"10.4103\/1008-682X.194420","article-title":"Sex determination and maintenance: The role of DMRT1 and FOXL2","volume":"19","author":"Huang","year":"2017","journal-title":"Asian J. Androl."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"14","DOI":"10.24272\/j.issn.2095-8137.2020.186","article-title":"Dmrt1 regulates the immune response by repressing the TLR4 signaling pathway in goat male germline stem cells","volume":"42","author":"Wei","year":"2021","journal-title":"Zool. Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1002\/dvdy.21409","article-title":"Sexual dimorphic expression of DMRT1 and Sox9a during gonadal differentiation and hormone-induced sex reversal in the teleost fish nile tilapia (Oreochromis niloticus)","volume":"237","author":"Kobayashi","year":"2008","journal-title":"Dev. Dyn."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/s10577-011-9264-x","article-title":"Dmrt1 mutation causes a male-to-female sex reversal after the sex determination by Dmy in the medaka","volume":"20","author":"Masuyama","year":"2012","journal-title":"Chromosom. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.ydbio.2016.12.008","article-title":"Dmrt1 is necessary for male sexual development in zebrafish","volume":"422","author":"Webster","year":"2017","journal-title":"Dev. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1007\/s10815-008-9270-x","article-title":"Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for japanese patients with azoospermia by meiotic arrest","volume":"25","author":"Miyamoto","year":"2008","journal-title":"J. Assist. Reprod. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.ajhg.2011.09.006","article-title":"XX ovarian dysgenesis is caused by a PSMC3IP\/HOP2 mutation that abolishes coactivation of estrogen-driven transcription","volume":"89","author":"Zangen","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1096\/fj.02-0463com","article-title":"Base excision repair capacity in mitochondria and nuclei: Tissue-specific variations","volume":"16","author":"Karahalil","year":"2002","journal-title":"FASEB J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/S0959-437X(97)80124-4","article-title":"DNA excision repair pathways","volume":"7","author":"Lindahl","year":"1997","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1095\/biolreprod55.3.630","article-title":"Xrcc-1 expression during male meiosis in the mouse","volume":"55","author":"Walter","year":"1996","journal-title":"Biol. Reprod."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1007\/BF02255837","article-title":"Testis and somatic Xrcc-1 DNA repair gene expression","volume":"20","author":"Walter","year":"1994","journal-title":"Somat. Cell Mol. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1128\/MCB.17.2.989","article-title":"An alternative splicing event which occurs in mouse pachytene spermatocytes generates a form of DNA ligase III with distinct biochemical properties that may function in meiotic recombination","volume":"17","author":"Mackey","year":"1997","journal-title":"Mol. Cell. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1095\/biolreprod46.2.201","article-title":"DNA polymerase-beta and poly (ADP) ribose polymerase mRNAs are differentially expressed during the development of male germinal cells","volume":"46","author":"Alcivar","year":"1992","journal-title":"Biol. Reprod."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1128\/MCB.22.7.2410-2418.2002","article-title":"Base excision repair is limited by different proteins in male germ cell nuclear extracts prepared from young and old mice","volume":"22","author":"Intano","year":"2002","journal-title":"Mol. Cell. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.ydbio.2013.01.031","article-title":"Constitutive activation of NOTCH1 signaling in Sertoli cells causes gonocyte exit from quiescence","volume":"377","author":"Garcia","year":"2013","journal-title":"Dev. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1089\/scd.2016.0318","article-title":"The NOTCH ligand JAG1 regulates GDNF expression in Sertoli cells","volume":"26","author":"Garcia","year":"2017","journal-title":"Stem Cells Dev."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Kami\u0144ska, A., Marek, S., Pardyak, L., Brzoskwinia, M., Bilinska, B., and Hejmej, A. (2020). Crosstalk between androgen-ZIP9 signaling and notch pathway in rodent sertoli cells. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21218275"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Wang, X., Guo, X., He, X., Di, R., Zhang, X., Zhang, J., and Chu, M. (2022). Integrated proteotranscriptomics of the hypothalamus reveals altered regulation associated with the FecB mutation in the BMPR1B gene that affects prolificacy in small tail han sheep. Biology, 12.","DOI":"10.3390\/biology12010072"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s10695-014-9992-x","article-title":"Molecular cloning and characterization of gonadotropin subunits (GTH\u03b1, FSH\u03b2 and LH\u03b2) and their regulation by hCG and GnRHa in Japanese sea bass (Lateolabrax japonicas) in vivo","volume":"41","author":"Chi","year":"2015","journal-title":"Fish Physiol. Biochem."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Mu, R., Yu, Y.Y., Gegen, T., Wen, D., Wang, F., Chen, Z., and Xu, W.B. (2021). Transcriptome analysis of ovary tissues from low- and high-yielding Changshun green-shell laying hens. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07688-x"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1068882","DOI":"10.3389\/fvets.2022.1068882","article-title":"Analysis of reproduction-related transcriptomes on pineal-hypothalamic-pituitary-ovarian tissues during estrus and anestrus in Tan sheep","volume":"9","author":"Wei","year":"2022","journal-title":"Front. Vet. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Ouyang, Q., Hu, S., Wang, G., Hu, J., Zhang, J., Li, L., Hu, B., He, H., Liu, H., and Xia, L. (2020). Comparative transcriptome analysis suggests key roles for 5-hydroxytryptamlne receptors in control of goose egg production. Genes, 11.","DOI":"10.3390\/genes11040455"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Fraser, H.M. (2006). Regulation of the ovarian follicular vasculature. Reprod. Biol. Endocrinol., 4.","DOI":"10.1186\/1477-7827-4-18"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1071\/RD08272","article-title":"SRB reproduction, fertility and development award lecture 2008. Regulation and manipulation of angiogenesis in the ovary and endometrium","volume":"21","author":"Fraser","year":"2009","journal-title":"Reprod. Fertil. Dev."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1093\/humupd\/dmr039","article-title":"Ovarian antral folliculogenesis during the human menstrual cycle: A review","volume":"18","author":"Baerwald","year":"2012","journal-title":"Hum. Reprod. Update"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"101630","DOI":"10.1016\/j.psj.2021.101630","article-title":"Polymorphism analysis and expression profile of the estrogen receptor 2 gene in leizhou black duck","volume":"101","author":"Asiamah","year":"2022","journal-title":"Poult. Sci."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/13\/23\/3690\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:32:58Z","timestamp":1760131978000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/13\/23\/3690"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,29]]},"references-count":46,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["ani13233690"],"URL":"https:\/\/doi.org\/10.3390\/ani13233690","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,29]]}}}