{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T05:01:29Z","timestamp":1780981289168,"version":"3.54.1"},"reference-count":60,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T00:00:00Z","timestamp":1780617600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2022YFD2401800"],"award-info":[{"award-number":["2022YFD2401800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012428","name":"Central Public-interest Scientific Institution Basal Research Fund, CAFS","doi-asserted-by":"crossref","award":["2026XK01"],"award-info":[{"award-number":["2026XK01"]}],"id":[{"id":"10.13039\/501100012428","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012428","name":"Central Public-interest Scientific Institution Basal Research Fund, CAFS","doi-asserted-by":"crossref","award":["2023TD38"],"award-info":[{"award-number":["2023TD38"]}],"id":[{"id":"10.13039\/501100012428","id-type":"DOI","asserted-by":"crossref"}]},{"name":"China-ASEAN Maritime Cooperation Fund","award":["CAMC-2018F"],"award-info":[{"award-number":["CAMC-2018F"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The zig-zag eel (Mastacembelus armatus) exhibits sexual dimorphism in growth patterns. Identifying the genes involved in sex differentiation is a crucial step toward achieving single-sex breeding and serves as a vital foundation for elucidating the XY sex determination mechanism in M. armatus. This study measured the morphological characteristics of male and female M. armatus and found that males were significantly superior to females in body weight and nearly all morphological indices. Subsequently, whole-transcriptome sequencing was performed on the gonads of adult males and females, identifying 11,714 DEmRNAs, 3442 DElncRNAs, 416 DEcircRNAs, and 620 DEmiRNAs, including male sex differentiation genes such as Sox30, Tbx1, Sox9, and Gata4, and female sex differentiation genes like Sox3, Foxl2, and Wnt4a. Functional enrichment analysis identified pathways associated with sex differentiation, including the TGF-beta signaling pathway, the steroid hormone biosynthesis, the Hippo signaling pathway, and the Wnt signaling pathway, etc. A ceRNA network was constructed based on differentially expressed mRNAs and ncRNAs, revealing that the sex differentiation-related genes Sox3, Sox9, Sox30, Tbx1, and Wt1 are regulated by one or multiple pairs of lncRNA\/circRNA-miRNA pairs. The study results will provide molecular targets for research on sex-controlled breeding in M. armatus and lay an important theoretical foundation for clarifying its sex differentiation mechanisms.<\/jats:p>","DOI":"10.3390\/ijms27115111","type":"journal-article","created":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T08:43:04Z","timestamp":1780648984000},"page":"5111","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Transcriptome Landscape of mRNAs, lncRNAs, circRNAs, and miRNAs Reveals Molecular Regulatory Networks of Sex Differentiation in the Zig-Zag Eel (Mastacembelus armatus)"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1190-2555","authenticated-orcid":false,"given":"Junxian","family":"Zhu","sequence":"first","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianghui","family":"Jia","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liqin","family":"Ji","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8572-0856","authenticated-orcid":false,"given":"Chen","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caixia","family":"Gao","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Laboratory Animals Monitoring Center (Guangdong Provincial Biotechnology Research Institute), Guangzhou 510663, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyou","family":"Hong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoli","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengqing","family":"Wei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinping","family":"Zhu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1146\/annurev-ento-120709-144828","article-title":"Evolution of sexual dimorphism in the Lepidoptera","volume":"56","author":"Allen","year":"2011","journal-title":"Annu. Rev. Entomol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.zool.2008.05.001","article-title":"Sexual dimorphism in bill morphology and feeding ecology in Cory\u2019s shearwater (Calonectris diomedea)","volume":"112","author":"Navarro","year":"2009","journal-title":"Zoology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"604000","DOI":"10.3389\/fimmu.2020.604000","article-title":"Sexual dimorphism in innate immunity: The role of sex hormones and epigenetics","volume":"11","author":"Shepherd","year":"2020","journal-title":"Front. Immunol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1113\/JP284342","article-title":"What\u2019s the difference? Understanding sexual dimorphism in physiology","volume":"601","author":"Hool","year":"2023","journal-title":"J. Physiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1534\/genetics.117.300294","article-title":"Sexual dimorphism and sex differences in Caenorhabditis elegans neuronal development and behavior","volume":"208","author":"Barr","year":"2018","journal-title":"Genetics"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"103070","DOI":"10.1016\/j.conb.2025.103070","article-title":"Sexual dimorphism in the behaviour and sensory systems of mosquitoes","volume":"93","author":"Bansal","year":"2025","journal-title":"Curr. Opin. Neurobiol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Zhu, J., Wang, Y., Chen, C., Ji, L., Hong, X., Liu, X., Chen, H., Wei, C., Zhu, X., and Li, W. (2024). Identification of sex-specific markers and candidate genes using WGS sequencing reveals a ZW-type sex-determination system in the Chinese soft-shell turtle (Pelodiscus sinensis). Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25020819"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Zhu, J., Ning, Y., Gao, C., Chen, C., Ji, L., Hong, X., Liu, X., Wei, C., Zhu, X., and Wang, X. (2026). Role of Col1a2 in collagen deposition in the carapace of the Chinese soft-shelled turtle (Pelodiscus sinensis): From molecular evolution to expression profile and then to function validation. Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27052160"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1007\/s11427-014-4797-9","article-title":"Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish","volume":"58","author":"Mei","year":"2015","journal-title":"Sci. China Life Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1007\/s11427-021-2075-x","article-title":"Sex determination mechanisms and sex control approaches in aquaculture animals","volume":"65","author":"Li","year":"2022","journal-title":"Sci. China Life Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"111804","DOI":"10.1016\/j.cbpa.2025.111804","article-title":"Evolutionary insights and expression patterns of sex-related gene families in the zig-zag eel Mastacembelus armatus","volume":"301","author":"Wang","year":"2025","journal-title":"Comp. Biochem. Physiol. A Mol. Integr. Physiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"735550","DOI":"10.1016\/j.aquaculture.2020.735550","article-title":"Screening and characterization of sex-specific markers by 2b-RAD sequencing in zig-zag eel (Mastacembelus armatus) with implication of XY sex determination system","volume":"528","author":"Xue","year":"2020","journal-title":"Aquaculture"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Zhu, J., Lei, L., Chen, C., Wang, Y., Liu, X., Geng, L., Li, R., Chen, H., Hong, X., and Yu, L. (2022). Whole-transcriptome analysis identifies gender dimorphic expressions of mRNAs and non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis). Biology, 11.","DOI":"10.3390\/biology11060834"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Liu, H., Zhang, J., Cui, T., Xia, W., Luo, Q., Fei, S., Zhu, X., Chen, K., Zhao, J., and Ou, M. (2024). Genome-wide association studies (GWAS) and transcriptome analysis reveal male heterogametic sex-determining regions and candidate genes in Northern snakeheads (Channa argus). Int. J. Mol. Sci., 25.","DOI":"10.2139\/ssrn.4939023"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"R93","DOI":"10.1530\/REP-15-0106","article-title":"The role of non-coding RNAs in male sex determination and differentiation","volume":"150","author":"Rastetter","year":"2015","journal-title":"Reproduction"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1093\/jeb\/voaf031","article-title":"Decoding Dmrt1: Insights into vertebrate sex determination and gonadal sex differentiation","volume":"38","author":"Ma","year":"2025","journal-title":"J. Evol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Wang, M.T., Li, Z., Ding, M., Yao, T.Z., Yang, S., Zhang, X.J., Miao, C., Du, W.X., Shi, Q., and Li, S. (2022). Two duplicated gsdf homeologs cooperatively regulate male differentiation by inhibiting cyp19a1a transcription in a hexaploid fish. PLoS Genet., 18.","DOI":"10.1371\/journal.pgen.1010288"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1159\/000447611","article-title":"Foxl2 and its relatives are evolutionary conserved players in gonadal sex differentiation","volume":"10","author":"Bertho","year":"2016","journal-title":"Sex. Dev."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1159\/000519237","article-title":"Non-coding RNAs: lncRNAs, miRNAs, and piRNAs in sexual development","volume":"15","author":"Burgos","year":"2021","journal-title":"Sex. Dev."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1101\/gr.275962.121","article-title":"ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation","volume":"32","author":"Tang","year":"2022","journal-title":"Genome Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.tibs.2014.02.007","article-title":"Enhancer RNAs and regulated transcriptional programs","volume":"39","author":"Lam","year":"2014","journal-title":"Trends Biochem. Sci."},{"key":"ref_22","first-page":"102376","article-title":"Cultivate YY supermale fish for the production of genetically all male zig-zag eel (Mastacembelus armatus) by MAS-GM technique","volume":"39","author":"Lu","year":"2024","journal-title":"Aquacult. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Cui, F.Y., Wang, Y.Y., Liang, H.Y., Yang, Y.X., Jiang, Z.Y., Song, J.H., Liu, C., Wu, Y.L., Mu, X.D., and Liu, Y. (2025). Comparative transcriptomic analysis of male and female gonads in the zig-zag eel (Mastacembelus armatus). Fishes, 10.","DOI":"10.3390\/fishes10030117"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"739498","DOI":"10.1016\/j.aquaculture.2023.739498","article-title":"Development of genetic sex markers of zig-zag eel (Mastacembelus armatus) by a NGS method","volume":"571","author":"Qin","year":"2023","journal-title":"Aquaculture"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Zhang, L.N., Chen, Y.M., Zhu, W.S., Sheng, H., Chen, W.K., Li, H.J., Cui, M.X., Han, C., and Shu, H. (2026). Sex-specific marker development and identification of an XY sex determination system in the tire track eel (Mastacembelus favus) via whole-genome resequencing. Animals, 16.","DOI":"10.3390\/ani16040605"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e13343","DOI":"10.1111\/acel.13343","article-title":"Identification of SRY-box 30 as an age-related essential gatekeeper for male germ-cell meiosis and differentiation","volume":"20","author":"Han","year":"2021","journal-title":"Aging Cell"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Tang, Y., Li, X., Xiao, H., Li, M., Li, Y., Wang, D., and Wei, L. (2019). Transcription of the Sox30 gene is positively regulated by Dmrt1 in Nile Tilapia. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20215487"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1016\/j.ygeno.2018.09.007","article-title":"Characterization and function of the T-box 1 gene in Chinese giant salamander Andrias davidianus","volume":"111","author":"Hu","year":"2019","journal-title":"Genomics"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Vining, B., Ming, Z., Bagheri-Fam, S., and Harley, V. (2021). Diverse regulation but conserved function: SOX9 in vertebrate sex determination. Genes, 12.","DOI":"10.3390\/genes12040486"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/s42003-025-07504-2","article-title":"GATA4 binding to the Sox9 enhancer mXYSRa\/Enh13 is critical for testis differentiation in mouse","volume":"8","author":"Ogawa","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Miura, I., Hasegawa, Y., Ito, M., Ezaz, T., and Ogata, M. (2024). Disruption of sex-linked Sox3 causes ZW female-to-male sex reversal in the Japanese frog Glandirana rugosa. Biomolecules, 14.","DOI":"10.3390\/biom14121566"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s12958-025-01377-0","article-title":"FOXL2 drives the differentiation of supporting gonadal cells in early ovarian development","volume":"23","author":"Danti","year":"2025","journal-title":"Reprod. Biol. Endocrinol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"R97","DOI":"10.1530\/REP-14-0177","article-title":"R-spondin1, WNT4, and the CTNNB1 signaling pathway: Strict control over ovarian differentiation","volume":"148","author":"Chassot","year":"2014","journal-title":"Reproduction"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1152\/physrev.00044.2019","article-title":"Sex determination, gonadal sex differentiation, and plasticity in vertebrate species","volume":"101","author":"Nagahama","year":"2021","journal-title":"Physiol. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/biolre\/ioaa218","article-title":"Igf3 is essential for ovary differentiation in zebrafish","volume":"104","author":"Xie","year":"2021","journal-title":"Biol. Reprod."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.semcdb.2008.10.004","article-title":"Steroid signaling and temperature-dependent sex determination-Reviewing the evidence for early action of estrogen during ovarian determination in turtles","volume":"20","author":"Ramsey","year":"2009","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"114561","DOI":"10.1016\/j.ygcen.2024.114561","article-title":"Transforming growth factor-\u03b2 (TGF-\u03b2): A master signal pathway in teleost sex determination","volume":"355","author":"Yu","year":"2024","journal-title":"Gen. Comp. Endocrinol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"bqz024","DOI":"10.1210\/endocr\/bqz024","article-title":"Gnrh3 regulates PGC proliferation and sex differentiation in developing zebrafish","volume":"161","author":"Feng","year":"2020","journal-title":"Endocrinology"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"R149","DOI":"10.1530\/REP-17-0408","article-title":"Stress and sex: Does cortisol mediate sex change in fish?","volume":"154","author":"Goikoetxea","year":"2017","journal-title":"Reproduction"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1093\/biolre\/iox057","article-title":"Yes-associated protein and WW-containing transcription regulator 1 regulate the expression of sex-determining genes in Sertoli cells, but their inactivation does not cause sex reversal","volume":"97","author":"Levasseur","year":"2017","journal-title":"Biol. Reprod."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S1673-8527(08)60107-1","article-title":"The human and mouse sex-determining SRY genes repress the Rspol\/beta-catenin signaling","volume":"36","author":"Lau","year":"2009","journal-title":"J. Genet. Genom."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"bqab066","DOI":"10.1210\/endocr\/bqab066","article-title":"Cholesterol contributes to male sex differentiation through its developmental role in androgen synthesis and hedgehog signaling","volume":"162","author":"Kothandapani","year":"2021","journal-title":"Endocrinology"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language?","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3809","DOI":"10.1038\/s41467-024-47658-x","article-title":"Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster","volume":"15","author":"Hurtado","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"He, Z., Ma, Z., Yang, D., Chen, Q., He, Z., Hu, J., Deng, F., Zhang, Q., He, J., and Ye, L. (2022). Circular RNA expression profiles and CircSnd1-miR-135b\/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08783-3"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s13059-021-02430-y","article-title":"Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair","volume":"22","author":"Xue","year":"2021","journal-title":"Genome Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: A fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e166","DOI":"10.1093\/nar\/gkt646","article-title":"Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts","volume":"41","author":"Sun","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_52","first-page":"e57","article-title":"FEELnc: A tool for long non-coding RNA annotation and its application to the dog transcriptome","volume":"45","author":"Wucher","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/s41467-019-13840-9","article-title":"Accurate quantification of circular RNAs identifies extensive circular isoform switching events","volume":"11","author":"Zhang","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: From microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/gkr688","article-title":"miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades","volume":"40","author":"Mackowiak","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Yang, J., Lu, B., Yu, Z., Zhang, L., Chen, Y., Chen, Z., Han, C., and Shu, H. (2024). Multiple tissues transcriptome of zig-zag eel (Mastacembelus armatus) with different growth rates. Animals, 14.","DOI":"10.3390\/ani14020248"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1461451","DOI":"10.3389\/fmars.2024.1461451","article-title":"Expression pattern of the fused in sarcoma gene and its contextual influence on the density-specific response of the growth hormone\/insulin-like growth factor 1 axis in zig-zag eels (Mastacembelus armatus)","volume":"11","author":"Xue","year":"2024","journal-title":"Front. Mar. Sci."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/11\/5111\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T04:55:11Z","timestamp":1780980911000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/11\/5111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,5]]},"references-count":60,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["ijms27115111"],"URL":"https:\/\/doi.org\/10.3390\/ijms27115111","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,5]]}}}