Koopman P. Gonad development: signals for sex. Curr Biol. 2001;11(12):R481–3.
Article
CAS
Google Scholar
Devlin RH, Nagahama Y. Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture. 2002;208(3–4):191–364.
Article
CAS
Google Scholar
Supiwong W, Pinthong K, Seetapan K, Saenjundaeng P, Bertollo LAC, de Oliveira EA, et al. Karyotype diversity and evolutionary trends in the Asian swamp eel Monopterus albus (Synbranchiformes, Synbranchidae): a case of chromosomal speciation? BMC Evol Biol. 2019;19(1):73.
Article
Google Scholar
CSY, China Statistical Yearbook. China statistical. Beijing: Publishing House; 2019
Liu C. Rudimentary hermaphroditism in the symbranchoid eel. Monopterus Javanensis. Sinensia. 1944;15:1e8.
Google Scholar
Hu Q, Xiao Q, Tian H, Li D, Li Z. Crucial role of dead end gene for primordial germ cell survival in rice field eel (Monopterus albus). Theriogenology. 2021;176:188–93.
Article
CAS
Google Scholar
Chen H, Liu H, Li R, Lin X, Luo D. Blood cell identification and hematological analysis during natural sex reversal in rice field eel (Monopterus albus). Aquaculture. 2021;538(11): 736543.
Article
CAS
Google Scholar
Yan T, Lu H, Sun C, Peng Y, Meng F, Gan R, et al. Nr5a homologues in the ricefield eel Monopterus albus: alternative splicing, tissue-specific expression, and differential roles on the activation of cyp19a1a promoter in vitro. Gen Comp Endocrinol. 2021;1(312): 113871.
Article
Google Scholar
Wang X, Lai F, Xiong J, Zhu W, Yuan B, Cheng H, et al. DNA methylation modification is associated with gonadal differentiation in Monopterus albus. Cell Biosci. 2020;10(1):129.
Article
Google Scholar
Kuroki S, Tachibana M. Epigenetic regulation of mammalian sex determination. Mol Cell Endocrinol. 2018;15(468):31–8.
Article
Google Scholar
Stévant I, Nef S. Genetic control of gonadal sex determination and development. Trends Genet. 2019;35(5):346–58.
Article
Google Scholar
Kojima-Kita K, Kuramochi-Miyagawa S, Nagamori I, Ogonuki N, Ogura A, Hasuwa H, et al. MIWI2 as an effector of DNA methylation and gene silencing in embryonic male germ cells. Cell Rep. 2016;16(11):2819–28.
Article
CAS
Google Scholar
Smallwood SA, Kelsey G. De novo DNA methylation: a germ cell perspective. Trends Genet. 2012;28(1):33–42.
Article
CAS
Google Scholar
Nishino K, Hattori N, Tanaka S, Shiota K. DNA methylation-mediated control of Sry gene expression in mouse gonadal development. J Biol Chem. 2004;279:22306.
Article
CAS
Google Scholar
Ge C, Ye J, Weber C, Sun W, Zhang H, Zhou Y, et al. The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species. Science. 2018;360(6389):645–8.
Article
CAS
Google Scholar
Navarro-Martín L, Viñas J, Ribas L, Díaz N, Gutiérrez A, Di Croce L, et al. DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperature-dependent sex ratio shifts in the European sea bass. PLoS Genet. 2011;7(12): e1002447.
Article
Google Scholar
Buenrostro JD, Wu B, Chang HY, Green leaf WJ. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21.
Article
Google Scholar
Yan F, Powell DR, Curtis DJ, Wong NC. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol. 2020;21(1):22.
Article
Google Scholar
Hu Q, Ao Q, Tan Y, Gan X, Luo Y, Zhu J. Genome-wide DNA methylation and RNA analysis reveal potential mechanism of resistance to Streptococcus agalactiae in GIFT strain of Nile Tilapia (Oreochromis niloticus). J Immunol. 2020;204(12):3182–90.
Article
CAS
Google Scholar
Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing. Nat Biotechnol. 2016;34:518–24.
Article
CAS
Google Scholar
Wick R, Judd LM, Holt KE. Comparison of Oxford Nanopore basecalling tools; 2018.
Li H. Minimap2:pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–100.
Article
CAS
Google Scholar
Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017;14(4):407–10.
Article
CAS
Google Scholar
Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, et al. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Nucleic Acids Res. 2016;44(1):75–94.
Article
Google Scholar
Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31(14):2382–3.
Article
CAS
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;12:550.
Article
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B. 1995;57:289–300.
Google Scholar
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001;29:1165–88.
Article
Google Scholar
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10(12):1213–8.
Article
CAS
Google Scholar
Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
Google Scholar
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44(W1):W160–5.
Article
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
Article
Google Scholar
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481(7381):389–93.
Article
CAS
Google Scholar
Hu QM, Tian HF, Xiao HB. Effects of temperature and sex steroids on sex ratio, growth, and growth-related gene expression in the Chinese giant salamander Andrias davidianus. Aquat Biol. 2019;28:79–90.
Article
Google Scholar
Hu QM, Meng Y, Tian HF, Zhang Y, Xiao HB. Sexually dimorphic expression of foxl2 and ftz-F1 in Chinese giant salamander Andrias davidianus. J Exp Zool B Mol Dev Evol. 2016;326(6):363–74.
Article
CAS
Google Scholar
Hu QM, Meng Y, Tian HF, Chen SL, Xiao HB. Cloning, expression of, and evidence of positive election for, the prolactin receptor gene in Chinese giant salamander (Andrias davidianus). J Exp Zool B Mol Dev Evol. 2015;324:707e19.
Article
Google Scholar
Hu QM, Xiao HB, Tian HF, Meng Y. Characterization and expression of cyp19a gene in the Chinese giant salamander Andrias davidianus. Comp Biochem Physiol B Biochem Mol Biol. 2016;192:219.
Article
Google Scholar
National Genomics Data Center and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in. Nucleic Acids Res. 2021;48(D1):D24–33.
Google Scholar
Tian HF, Hu QM, Li Z. A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data. Gene. 2021;11(1):jkaa032.
CAS
Google Scholar
Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, et al. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet. 2014;46(3):253–60.
Article
CAS
Google Scholar
Garcia-Moreno SA, Futtner CR, Salamone IM, Gonen N, Lovell-Badge R, Maatouk DM. Gonadal supporting cells acquire sex-specific chromatin landscapes during mammalian sex determination. Dev Biol. 2019;446(2):168–79.
Article
CAS
Google Scholar
Cheng H, Guo Y, Yu Q, Zhou R. The rice feld eel as a model system for vertebrate sexual development. Cytogenet Genome Res. 2003;101(3–4):274–7.
Article
CAS
Google Scholar
Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, et al. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Genome Biol. 2020;21(1):52.
Article
CAS
Google Scholar
Lin CS, Park T, Chen ZP, Leavitt J. Human plastin genes Comparative gene structure, chromosome location, and differential expression in normal and neoplastic cells. J Biol Chem. 1993;268:2781e2792.
Google Scholar
Wabnitz G, Balta E, Samstag Y. L-plastin regulates the stability of the immune synapse of naive and effector T-cells. Adv Biol Regul. 2017;63:107–14.
Article
CAS
Google Scholar
Qin H, Li X, Wang J, Sun G, Mu X, Ji R. Ovarian transcriptome profile from pre-laying period to broody period of Xupu goose. Poult Sci. 2021;100(10): 101403.
Article
CAS
Google Scholar
Sha S, Bhatia H, Yoon S. An RNA-seq based transcriptomic investigation into the productivity and growth variants with Chinese hamster ovary cells. J Biotechnol. 2018;271:37–46.
Article
CAS
Google Scholar
Zheng JP, Rudra-Ganguly N, Miller GJ, Moffatt KA, Roy-Burman P. Steroid hormone induction and expression patterns of l-plastin in normal and carcinomatous prostate tissues. Am J Pathol. 1997;150(6):2009–18.
CAS
Google Scholar
Shinomiya H. Plastin family of actin-bundling proteins: its functions in leukocytes, neurons, intestines, and cancer. Int J Cell Biol. 2012;2012: 213492.
Article
Google Scholar
Hurd AJ, Whitmarsh GS, Baldwin SM, Kelly JP, Waltho NC, Price BA, et al. Hornby mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone. J Mol Biol. 1999;286:389–401.
Article
CAS
Google Scholar
Mustapha UF, Assan D, Huang YQ, Li GL, Jiang DN. High polymorphism in the dmrt2a gene is incompletely sex-linked in spotted scat, Scatophagus argus. Animals. 2022;12(5):613.
Article
Google Scholar
Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, et al. The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature. 2009;461(7261):267–71.
Article
CAS
Google Scholar
Boulanger L, Pannetier M, Gall L, Allais-Bonnet A, Elzaiat M, Le Bourhis D, et al. FOXL2 is a female sex-determining gene in the goat. Curr Biol. 2014;24(4):404–8.
Article
CAS
Google Scholar
Jones P, Takai D. The role of DNA methylation in mammalian epigenetics. Science. 2001;293(5532):1068–70.
Article
CAS
Google Scholar
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 2007;39(1):61–9.
Article
CAS
Google Scholar