De novo transcriptome sequencing to identify the sex-determination genes in Hyriopsis schlegelii

References

• Kashimada K, Koopman P. Sry: the master switch in mammalian sex determination. Development. 2010;137:3921–3930.10.1242/dev.048983
   PubMed Web of Science ®Google Scholar
• Jakob S, Lovell-Badge R. Sex determination and the control of Sox9 expression in mammals. FEBS J. 2011;278:1002–1009.10.1111/j.1742-4658.2011.08029.x
   PubMed Web of Science ®Google Scholar
• Kopp A. Dmrt genes in the development and evolution of sexual dimorphism. Trends in Genet. 2012;28:175–184.10.1016/j.tig.2012.02.002
   PubMed Web of Science ®Google Scholar
• Uhlenhaut NH, Jakob S, Anlag K, Eisenberger T, Sekido R, Kress J, Treier AC, Klugmann C, Klasen C, Holter NI, Riethmacher D, Schütz G, Cooney AJ, Lovell-Badge R, Treier M. Somatic sex reprogramming of adult ovaries to testes by FOXL2 ablation. Cell. 2009;139:1130–1142.
   PubMed Web of Science ®Google Scholar
• Chassot AA, Gregoire EP, Lavery R, Taketo MM, de Rooij DG, Adams IR, Chaboissier MC. RSPO1/β-catenin signaling pathway regulates oogonia differentiation and entry into meiosis in the mouse fetal ovary. PLoS One. 2011;6:e25641.10.1371/journal.pone.0025641
   Google Scholar
• Lu H, Huang X, Zhang L, Guo Y, Cheng H, Zhou R. Multiple alternative splicing of mouse Dmrt1 during gonadal differentiation. chem. Biophys. Res. Commun. 2007;352:630–634.10.1016/j.bbrc.2006.11.066
   PubMed Web of Science ®Google Scholar
• Chue J, Smith CA. Sex determination and sexual differentiation in the avian model. FEBS J. 2011;278:1027–1034.10.1111/j.1742-4658.2011.08032.x
   PubMed Web of Science ®Google Scholar
• Aoyama S, Shibata K, Tokunaga S, Takase M, Matsui K, Nakamura M. Expression of Dmrt1 protein in developing and in sex-reversed gonads of amphibians. Cytogenet. Genome Res. 2003;101:295–301.10.1159/000074352
   PubMed Web of Science ®Google Scholar
• Herpin A, Schartl M. Dmrt1 genes at the crossroads: a widespread and central class of sexual development factors in fish. FEBS J. 2011;278:1010–1019.10.1111/j.1742-4658.2011.08030.x
   PubMed Web of Science ®Google Scholar
• Wilhelm D, Hiramatsu R, Mizusaki H, Widjaja L, Combes AN, Kanai Y, Koopman P. SOX9 regulates prostaglandin d synthase gene transcription in vivo to ensure testis development. J. Biol. Chem. 2007;282:10553–10560.10.1074/jbc.M609578200
   PubMed Web of Science ®Google Scholar
• Sekido R, Lovell-Badge R. Sex determination and SRY: down to a wink and a nudge? Trends in Genet. 2009;25:19–29.10.1016/j.tig.2008.10.008
   PubMed Web of Science ®Google Scholar
• Jiang T, Hou CC, She ZY, Yang WX. The SOX gene family: function and regulation in testis determination and male fertility maintenance. Mol. Biol. Rep. 2013;40:2187–2194.10.1007/s11033-012-2279-3
   PubMed Web of Science ®Google Scholar
• Hempel LU, Oliver B. Sex-specific DoublesexM expression in subsets of Drosophila somatic gonad cells. BMC. Dev. Biol. 2007;7:113.10.1186/1471-213X-7-113
   PubMed Web of Science ®Google Scholar
• Yi W, Ross JM, Zarkower D. Mab-3 is a direct tra-1 target gene regulating diverse aspects of C. elegans male sexual development and behavior. Development. 2000;127:4469–4480.
   PubMed Web of Science ®Google Scholar
• Starostina NG, Lim JM, Schvarzstein M, Wells L, Spence AM, Kipreos ET. A CUL-2 ubiquitin ligase containing three FEM proteins degrades TRA-1 to regulate C. elegans sex determination. Dev. Cell. 2007;13:127–139.10.1016/j.devcel.2007.05.008
   PubMed Web of Science ®Google Scholar
• Haag ES, Wang S, Kimble J. Rapid coevolution of the Nematode sex-determining genes fem-3 and tra-2. Current Biol. 2002;12:2035–2041.10.1016/S0960-9822(02)01333-7
   PubMed Web of Science ®Google Scholar
• Yu Y, Hong YJ, Qiu QJ, Wang JH, Xu MX, Li YJ. Embryonic development and breading-season gonad in Hyriopsis schlegeli. Chn. J. Zool. 2008;43:102–107.
   Google Scholar
• Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 2011;29:644–652.
   PubMed Web of Science ®Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–3676.10.1093/bioinformatics/bti610
   PubMed Web of Science ®Google Scholar
• Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34:W293–W297.
   PubMed Web of Science ®Google Scholar
• Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods. 2008;5:621–628.10.1038/nmeth.1226
   PubMed Web of Science ®Google Scholar
• Audic S, Claverie JM. The significance of digital gene expression profiles. Genome. Res. 1997;7:986–995.
   PubMed Web of Science ®Google Scholar
• Shi JW, Peng K, Sheng JQ, Wang JH, Yi WJ, Wu HJ, Gu Q, Hong YJ. A specific genomic organization and a novel promoter sequence for both ZP2 and ZP3 gene expressions in the Pingxiang red transparent crucian carp, Carassius auratus var. pingxiangnensis. Comp. Biochem. Physiol. D: Genomics Proteomics. 2013;8:275–282.
   PubMed Web of Science ®Google Scholar
• Shi JW, Sheng JQ, Peng K, Wang JH, Yi WJ, Wu HJ, Gu Q, Hong YJ. Expression pattern of the zona pellucida 3 (ZP3) gene during ovarian development and the location of ZP3 protein in oocytes in a natural, wild triploid crucian carp mutant, Carassius auratus var. Pingxiangnensis. Genet. Mol. Res. 2013;12:5640–5650.10.4238/2013.November.18.13
   PubMed Web of Science ®Google Scholar
• Schefe JH, Lehmann KE, Buschmann IR, Unger T, Funke-Kaiser H. Quantitative real-time RT-PCR data analysis: current concepts and the novel “gene expression’s C T difference” formula. J. Mol. Med. 2006;84:901–910.10.1007/s00109-006-0097-6
   PubMed Web of Science ®Google Scholar
• Feng B, Dong L, Niu D, Meng S, Zhang B, Liu D, Hu S, Li J. Identification of immune genes of the Agamaki Clam (Sinonovacula constricta) by sequencing and bioinformatic analysis of ESTs. Mar. Biotechnol. 2010;12:282–291.10.1007/s10126-009-9216-z
   PubMed Web of Science ®Google Scholar
• Huan P, Wang HX, Liu BZ. Transcriptomic analysis of the clam Meretrix meretrix on different larval stages. Mar. Biotechnol. 2012;14:69–78.10.1007/s10126-011-9389-0
   PubMed Web of Science ®Google Scholar
• Ferguson-Smith M. The evolution of sex chromosomes and sex determination in vertebrates and the key role of DMRT1. Sex. Dev. 2007;1:2–11.10.1159/000096234
   PubMed Web of Science ®Google Scholar
• Wilhelm D. R-spondin1-discovery of the long-missing, mammalian female-determining gene? BioEssays. 2007;29:314–318.10.1002/(ISSN)1521-1878
   PubMed Web of Science ®Google Scholar
• Miyamoto Y, Taniguchi H, Hamel F, Silversides DW, Viger RS. A GATA4/WT1 cooperation regulates transcription of genes required for mammalian sex determination and differentiation. BMC Mol. Biol. 2008;9:44.10.1186/1471-2199-9-44
   PubMed Web of Science ®Google Scholar
• Kocer A, Pinheiro I, Pannetier M, Renault L, Parma P, Radi O, Kim KA, Camerino G, Pailhoux E. R-spondin1 and FOXL2 act into two distinct cellular types during goat ovarian differentiation. BMC Dev. Biol. 2008;8:36.10.1186/1471-213X-8-36
   PubMed Web of Science ®Google Scholar
• Matsumoto Y, Crews D. Molecular mechanisms of temperature-dependent sex determination in the context of ecological developmental biology. Mol. Cell. Endocrinol. 2012;354:103–110.10.1016/j.mce.2011.10.012
   PubMed Web of Science ®Google Scholar
• Lau YFC, Li YM. The human and mouse sex-determining SRY genes repress the Rspol/β-catenin signaling. J. Genet. Genomics. 2009;36:193–202.10.1016/S1673-8527(08)60107-1
   PubMed Web of Science ®Google Scholar
• Tomaselli S, Megiorni F, Lin L, Mazzilli MC, Gerrelli D, Majore S, Grammatico P, Achermann JC. Human RSPO1/R-spondin1 is expressed during early ovary development and augments β-catenin signaling. PLoS ONE. 2011;6:e16366.10.1371/journal.pone.0016366
   Google Scholar
• Baker BS, Gorman M, Marin I. Dosage compensation in Drosophila. Annu. Rev. Genet. 1994;28:491–521.10.1146/annurev.ge.28.120194.002423
   PubMed Web of Science ®Google Scholar
• Marín I, Siegal ML, Baker BS. The evolution of dosage-compensation mechanisms. BioEssays. 2000;22:1106–1114.10.1002/1521-1878(200012)22:12<>1.0.CO;2-8
   PubMed Web of Science ®Google Scholar
• Legube G, McWeeney SK, Lercher MJ, Akhtar A. X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev. 2006;20:871–883.10.1101/gad.377506
   PubMed Web of Science ®Google Scholar
• Madl JE, Herman RK. Polyploids and sex determination in Caenorhabditis elegans. Genetics. 1979;93:393–402.
   PubMed Web of Science ®Google Scholar