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Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome

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Abstract

The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased. Several sex-related pathways were observed, including the Wnt signaling pathway. After elevated temperature and estrogen exposure, neomale and neofemale specimens were identified by a female-specific marker for the first time. RT-qPCR analysis showed the expression profile of ten selected sex-biased genes to be exhibited consistently in male and neomale and in female and neofemale, with the exception of the Amh and TfIIIa genes. Results suggested that these genes may play important roles in A. davidianus sex determination and gonad development. This provides a basis for further investigation of the molecular mechanisms of sex determination in amphibians.

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References

  • Akçurin S, Türkkahraman D, Kim WY, Durmaz E, Shin JG, Lee SJ (2016) A novel null mutation in P450 aromatase gene (CYP19A1) associated with the development of hypoplastic ovaries in humans. J Clin Res Pediatr Endocrinol 8(2):205–210

    Article  PubMed  PubMed Central  Google Scholar 

  • Alam MA, Kobayashi Y, Horiguchi R, Hirai T, Nakamura M (2008) Molecular cloning and quantitative expression of sexually dimorphic markers Dmrt1 and Foxl2 during female-to-male sex change in Epinephelus merra. Gen Comp Endocrinol 157(1):75–85

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986

    Article  CAS  PubMed  Google Scholar 

  • Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188

    Article  Google Scholar 

  • Blower MD, Jambhekar A, Schwarz DS, Toombs JA (2013) Combining different mRNA capture methods to analyze the transcriptome: analysis of the Xenopus laevis transcriptome. Plos One 8:e77700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boerboom D (2009) Paracrine signalling in the ovary: the role of Wnt. Endocr Abstracts 19:S21

    Google Scholar 

  • Boulanger L, Pannetier M, Gall L, Allais-Bonnet A, Elzaiat M, Le Bourhis D, Daniel N, Richard C, Cotinot C, Ghyselinck NB, Pailhoux E (2014) FOXL2 is a female sex-determining gene in the goat.Curr Biol, 24: 404–408

  • Bowles J, Knight D, Smith C, Wilhelm D, Richman J, Mamiya S, Yashiro K, Chawengsaksophak K, Wilson MJ, Rossant J, Hamada H, Koopman P (2006) Retinoid signaling determines germ cell fate in mice. Science 312(5773):596–600

    Article  CAS  PubMed  Google Scholar 

  • Boyer A, Goff AK, Boerboom D (2010) WNT signaling in ovarian follicle biology and tumorigenesis. Trends Endocrinol Metab 21(1):25–32

    Article  CAS  PubMed  Google Scholar 

  • Brelsford A, Stöck M, Betto-Colliard C, Dubey S, Dufresnes C, Jourdan-Pineau H, Rodrigues N, Savary R, Sermier R, Perrin N (2013) Homologous sex chromosomes in three deeply divergent anuran species. Evolution 67:2434–2440

    Article  PubMed  Google Scholar 

  • Che RB, Sun YN, Wang RX, Xu TJ (2014) Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers. Plos One 9:e87940

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen SL, Zhang GJ, Shao CW, Huang QF, Liu G, Zhang P, Song WT, An N, Chalopin D, Volff JN, Hong YH, Li QY, Sha ZX, Zhou HL, Xie MS, Yu QL, Liu Y, Xiang H, Wang N, Wu K, Yang CG, Zhou Q, Liao XL, Yang LF, Hu QM, Zhang JL, Meng L, Jin LJ, Tian YS, Lian JM, Yang JF, Miao GD, Liu SS, Liang Z, Yan F, Li YZ, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao YW, Schartl M, Tang QS, Wang J (2014a) Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 46:253–260

    Article  CAS  PubMed  Google Scholar 

  • Chen X, Mei J, Wu J, Jing J, Ma W, Zhang J, Dan C, Wang W, Gui JF (2014b) A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish. Mar Biotechnol 17:190–198

    Article  CAS  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Dong XL, Chen SL, Ji XS, Shao CW (2011) Molecular cloning, characterization and expression analysis of Sox9a and Foxl2 genes in half-smooth tongue sole (Cynoglossus semilaevis). Acta Oceanol Sin 30(1):68–77

    Article  CAS  Google Scholar 

  • Dournon C, Houillon C (1985) Thermosensibilite de la differenciation sexuelle chez l’Amphibien Urodele Pleurodeles waitlii Michah. Conditions pour obtenir rinversion du phenotype sexuel de toutes les femelles genetiques sous raction de la temperature d’elevage. Reprod Nutr Dev 25:671–688

    Article  Google Scholar 

  • Feng RJ, Fang LJ, Cheng YY, He X, Jiang WT, Dong RR, Shi HJ, Jiang DN, Sun LN, Wang DS (2015) Retinoic acid homeostasis through aldh1a2 and cyp26a1 mediates meiotic entry in Nile tilapia (Oreochromis niloticus). Sci Rep 5:10131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao KQ. Shubin NH (2003) Earliest known crown-group salamanders. Nature 422:424–428

    Article  CAS  PubMed  Google Scholar 

  • Gao LL, Zhou CX, Zhang XL, Liu P, Jin Z, Zhu GY, Ma Y, Li J, Yang ZX, Zhang D (2017) ZP3 is required for germinal vesicle breakdown in mouse oocyte meiosis. Sci Rep 7:41272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geng XF, Li WS, Shang HT, Gou Q, Zhang FC, Zang XY, Zeng BH, Li J, Wang Y, Ma J, Guo JL, Jian JB, Chen B, Qiao ZG, Zhou MH, Wei H, Fang XD, Xu CS (2017) A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. Gigascience 6:1–7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gregory TR (2002) Genome size and developmental complexity. Genetica 115:131–146

    Article  PubMed  Google Scholar 

  • Haselman JT, Olmstead AW, Degitz SJ (2015) Global gene expression during early differentiation of Xenopus (Silurana) tropicalis gonad tissues. Gen Comp Endocrinol 214:103–113

    Article  CAS  PubMed  Google Scholar 

  • Hattori RS, Murai Y, Oura M, Masuda S, Majhi SK, Sakamoto T, Fernandino JI, Somoza GM, Yokota M, Strüssmann CA (2012) A Y-linked anti-mullerian hormone duplication takes over a critical role in sex determination. Proc Natl Acad Sci USA 109:2955–295932

    Article  PubMed  PubMed Central  Google Scholar 

  • Hillis DM, Green DM (1990) Evolutionary changes of heterogametic sex in the phylogenetic history of amphibians. J Evol Biol 3:49–64

    Article  Google Scholar 

  • Hu QM, Xiao HB, Tian HF, Meng Y (2016a) Characterization and expression of cyp19a gene in the Chinese giant salamander Andrias davidianus. Comp Biochem Physiol B Biochem Mol Biol 192:21–29

    Article  CAS  PubMed  Google Scholar 

  • Hu QM, Meng Y, Tian HF, Zhang Y, Xiao HB (2016b) Sexually dimorphic expression of Foxl2 and Ftz-F1 in chinese giant salamander Andrias davidianus. J Exp Zool B Mol Dev Evol 326(6):363–374

    Article  CAS  PubMed  Google Scholar 

  • Huang Y, Gao XC, Xiong JL, Ren HT, Sun XH (2017) Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus). Genom Data 12:109–110

    Article  PubMed  PubMed Central  Google Scholar 

  • Keinath MC, Timoshevskiy VA, Timoshevskaya NY, Tsonis PA, Voss SR, Smith JJ (2015) Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep 5:16413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koopman P, Gubbay J, Vivian N, Goodfellow P, Lovell-Badge R (1991) Male development of chromosomally female mice transgenic for Sry. Nature 351:117–121

    Article  CAS  PubMed  Google Scholar 

  • Lau EL, Lee MF, Chang CF (2013) Conserved sex-specific timing of meiotic initiation during sex differentiation in the Protandrous Black Porgy Acanthopagrus schlegelii. Biol Reprod 88(6):150

    Article  PubMed  Google Scholar 

  • Li FG, Wang LX, Lan QJ, Yang H, Li Y, Liu XL, Yang ZX (2015) RNA-Seq analysis and gene discovery of Andrias davidianus using illumina short read sequencing. Plos One 10:e0123730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu WQ, Li KM, Bai DD, Yin JQ, Tang YY, Chi FL, Zhang LF, Wang Y, Pan JP, Liang SS, Guo Y, Ruan JL, Kou XC, Zhao YH, Wang H, Chen JY, Teng XM, Gao SR (2017) Dosage effects of ZP2 and ZP3 heterozygous mutations cause human infertility. Hum Genet 136(8):975–985

    Article  CAS  PubMed  Google Scholar 

  • Maruo K, Suda M, Yokoyama S, Oshima Y, Nakamura M (2008) Steroidogenic gene expression during sex determination in the frog Rana rugosa. Gen Comp Endocrinol 158:87–94

    Article  CAS  PubMed  Google Scholar 

  • Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, Kobayashi T, Morrey CE, Shibata N, Asakawa S, Shimizu N, Hori H, Hamaguchi S, Sakaizumi M (2002) DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature 417:559–563

    Article  CAS  PubMed  Google Scholar 

  • Monkley SJ, Delaney SJ, Pennisi DJ, Christiansen JH, Wainwright BJ (1996) Targeted disruption of the Wnt2 gene results in placentation defects. Development 122(11):3343–3353

    CAS  PubMed  Google Scholar 

  • Mork L, Capel B (2015) Conserved action of β-catenin during female fate determination in the red-eared slider turtle. Evol Dev 15(2):96–106

    Article  CAS  Google Scholar 

  • Nakamura K, Islam MR, Takayanagi M, Yasumuro H, Inami W, Kunahong A, Casco-Robles RM, Toyama F, Chiba C (2014) A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster. Plos One 9:e109831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nicol B, Guiguen Y (2011) Expression profiling of Wnt signaling genes during gonadal differentiation and gametogenesis in rainbow trout. Sex Dev 5:318–329

    Article  CAS  PubMed  Google Scholar 

  • Oshima Y, Kato T, Wang DS, Murakami T, Matsuda Y, Nagahama Y, Nakamura M (2006) Promoter activity and chromosomal location of the Rana rugosa P450 aromatase (CYP19) gene. Zoolog Sci 23:79–85

    Article  CAS  PubMed  Google Scholar 

  • Ramsey M, Shoemaker C, Crews D (2007) Gonadal expression of Sf1 and aromatase during sex determination in the red-eared slider turtle (Trachemys scripta), a reptile with temperature-dependent sex determination. Differentiation 75:978–991

    Article  CAS  PubMed  Google Scholar 

  • Recknagel H, Elmer KR, Meyer A (2013) A hybrid genetic linkage map of two ecologically and morphologically divergent midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq). G3 (Bethesda), 3(1):65–74

  • Robertson LS, Cornman RS (2014) Transcriptome resources for the frogs Lithobates clamitans and Pseudacris regilla, emphasizing antimicrobial peptides and conserved loci for phylogenetics. Mol Ecol Resour 14:178–183

    Article  CAS  PubMed  Google Scholar 

  • Savage AE, Kiemnec-Tyburczy KM, Ellison AR, Fleischer RC, Zamudio KR (2014) Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 542:98–108

    Article  CAS  PubMed  Google Scholar 

  • Sessions SK, Pedro EL, James K (1982) Cytogenetics of the Chinese giant salamander Andrias davidianus (Blanchard: the evolutionary significance of cryptobranchoid karyotypes. Chromosoma 86:341–357

    Article  Google Scholar 

  • Smith JJ, Voss SR (2009) Amphibian sex determination: segregation and linkage analysis using members of the tiger salamander species complex (Ambystoma mexicanum and A. t. tigrinum). Heredity 102(6):542–548

    Article  CAS  PubMed  Google Scholar 

  • Smith CA, Katz M, Sinclair AH (2003) DMRT1 is upregulated in the gonads during female-to-male sex reversal in ZW chicken embryos. Biol Reprod 68(2):560–570

    Article  CAS  PubMed  Google Scholar 

  • Smith JJ, Kump DK, Walker JA, Parichy DM, Voss SR (2005) A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. Genetics 171(3):1161–1171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, Sinclair AH (2009) The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature 461:267–271

    Article  CAS  PubMed  Google Scholar 

  • Tao WJ, Yuan J, Zhou LY, Sun LN, Sun YL, Yang SJ, Li MH, Zeng S, Huang BF, Wang DS (2013) Characterization of gonadal transcriptomes from nile tilapia (Oreochromis niloticus) reveals differentially expressed genes. Plos One 8:e63604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trant JM, Gavasso S, Ackers J, Chung BC, Place AR (2001) Developmental expression of cytochrome P450 aromatase genes (CYP19a and CYP19b) in zebrafish fry (Danio rerio). J Exp Zool 290(5):475–483

    Article  CAS  PubMed  Google Scholar 

  • Vainio S, Heikkilä M, Kispert A, Chin N, McMahon AP (1999a) Female development in mammals is regulated by Wnt-4 signalling. Nature 397(6718):405–409

    Article  CAS  PubMed  Google Scholar 

  • Vainio S, Heikkila M, Kispert A, Chin N, McMahon AP (1999b) Female development in mammals is regulated by Wnt4 signalling. Nature 397:405–409

    Article  CAS  PubMed  Google Scholar 

  • Val P, Lefrançois-Martinez AM, Veyssière G, Martinez A (2003) SF-1 a key player in the development and differentiation of steroidogenic tissues. Nucl Recept 1:8–30

    Article  PubMed  PubMed Central  Google Scholar 

  • Vinogradov AE (1998) Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31:100–109

    Article  CAS  PubMed  Google Scholar 

  • Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Basa S, Walker JA, Smith JJ (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res 21:1306–1312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wallace H, Badawy GM, Wallace BM (1999) Amphibian sex determination and sex reversal. Cell Mol Life Sci 55:901–909

    Article  CAS  PubMed  Google Scholar 

  • Wang DS, Kobayashi T, Zhou LY, Paul-Prasanth B, Ijiri S, Sakai F, Okubo K, Morohashi K, Nagahama Y (2007) Foxl2 up-regulates aromatase gene transcription in a female-specific manner by binding to the promoter as well as interacting with Ad4 Binding Protein/Steroidogenic Factor 1. Mol Endocrinol 21(3):712–725

    Article  CAS  PubMed  Google Scholar 

  • Wu GC, Chang CF (2009) Wnt4 Is associated with the development of ovarian tissue in the protandrous black Porgy, Acanthopagrus schlegelii. Biol Reprod 81:1073–1082

    Article  CAS  PubMed  Google Scholar 

  • Yang WZ, Qi Y, Bi K, Fu JZ (2012) Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. Kukunoris. BMC Genom 13:588

    Article  CAS  Google Scholar 

  • Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:293–297

    Article  Google Scholar 

  • Yin YK, Tang HP, Liu Y, Chen Y, Li GF, Liu XC, Lin HR (2017) Targeted disruption of aromatase reveals dual functions of cyp19a1a during sex differentiation in zebrafish. Endocrinology

  • Yoshimoto S, Okada E, Umemoto H, Tamura K, Uno Y, Nishida-Umehara C, Matsuda Y, Takamatsu N, Shiba T, Ito M (2008) A W-linked DM-domain gene,DM-W,participates in primary ovary development in Xenopus laevis. Proc Natl Acad Sci USA 105:2469–2474

    Article  PubMed  PubMed Central  Google Scholar 

  • Yoshiura Y, Senthilkumaran B, Watanabe M, Oba Y, Kobayashi T, Nagahama Y (2003) Synergistic expression of Ad4BP/Ad4BP/SF-1 and cytochrome P-450 aromatase(ovarian type) in the ovary of Nile tilapia, Oreochromis niloticus, during vitellogenesis suggests transcriptional interaction. Biol Reprod 68:1545–1553

    Article  CAS  PubMed  Google Scholar 

  • Zhu B, Feng Z, Qu A, Gao H, Zhang Y, Sun D, Song W, Saura A (2002) Brief report. The karyotype of the caudate amphibian, Andrias davidianus. Hereditas 136:85–88

    Article  PubMed  Google Scholar 

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Acknowledgements

The authors would like to thank the Linen lab group for comments on data analysis. This work was supported by National Nature Science Foundation of China (31502155), Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences (KF-2017-06), National Nonprofit Institute Research Grant (2017JBF0205).

Funding

This work was supported by National Nature Science Foundation of China (31502155), Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences (KF-2017-06), National Nonprofit Institute Research Grant (2017JBF0205).

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  1. Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China

    Qiaomu Hu, Haifeng Tian, Yan Meng, Quanhe Wang & Hanbing Xiao

  2. College of Life Science, Yangtze University, Jingzhou, 434025, China

    Wei Li & Quanhe Wang

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  1. Qiaomu Hu
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  2. Haifeng Tian
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  3. Wei Li
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  4. Yan Meng
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Hu, Q., Tian, H., Li, W. et al. Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome. Mol Genet Genomics 294, 287–299 (2019). https://doi.org/10.1007/s00438-018-1508-4

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