title: The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo).
abstract: BACKGROUND
  Teleosts are characterized by a remarkable breadth of sexual mechanisms including various forms of hermaphroditism. Sparidae is a fish family exhibiting gonochorism or hermaphroditism even in closely related species. The sparid Diplodus puntazzo (sharpsnout seabream), exhibits rudimentary hermaphroditism characterized by intersexual immature gonads but single-sex mature ones. Apart from the intriguing reproductive biology, it is economically important with a continuously growing aquaculture in the Mediterranean Sea, but limited available genetic resources. Our aim was to characterize the expressed transcriptome of gonads and brains through RNA-Sequencing and explore the properties of genes that exhibit sex-biased expression profiles.
  
  
  RESULTS
  Through RNA-Sequencing we obtained an assembled transcriptome of 82,331 loci. The expression analysis uncovered remarkable differences between male and female gonads, while male and female brains were almost identical. Focused search for known targets of sex determination and differentiation in vertebrates built the sex-specific expression profile of sharpsnout seabream. Finally, a thorough genetic marker discovery pipeline led to the retrieval of 85,189 SNPs and 29,076 microsatellites enriching the available genetic markers for this species.
  
  
  CONCLUSIONS
  We obtained a nearly complete source of transcriptomic sequence as well as marker information for sharpsnout seabream, laying the ground for understanding the complex process of sex differentiation of this economically valuable species. The genes involved include known candidates from other vertebrate species, suggesting a conservation of the toolkit between gonochorists and hermaphrodites.
authors.forename: Tereza
authors.initials: T
authors.lastname: Manousaki
authors.forename: Alexandros
authors.initials: A
authors.lastname: Tsakogiannis
authors.forename: Jacques
authors.initials: J
authors.lastname: Lagnel
authors.forename: Elena
authors.initials: E
authors.lastname: Sarropoulou
authors.forename: Jenny Z
authors.initials: JZ
authors.lastname: Xiang
authors.forename: Nikos
authors.initials: N
authors.lastname: Papandroulakis
authors.forename: Constantinos C
authors.initials: CC
authors.lastname: Mylonas
authors.affiliation: Institute of Marine Biology, Biotechnology and Aquaculture (I,M,B,B,C,), Hellenic Centre for Marine Research (H,C,M,R,), Heraklion, Greece. tsigeno@hcmr.gr.
authors.forename: Costas S
authors.initials: CS
authors.lastname: Tsigenopoulos
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D012734:Disorders of Sex Development / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D010053:Ovary / Q000378:metabolism; D021541:Sea Bream / Q000235:genetics*; D012727:Sex Characteristics; D019849:Sex Determination Processes / Q000235:genetics; D012733:Sex Differentiation / Q000235:genetics; D013737:Testis / Q000378:metabolism
references.citation: Eur J Neurosci. 2010 Dec;32(12):2105-15
references.pmid: 21143665
references.citation: Bioinformatics. 2011 Aug 1;27(15):2156-8
references.pmid: 21653522
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2469-74
references.pmid: 18268317
references.citation: PLoS One. 2008 Jul 30;3(7):e2837
references.pmid: 18665231
references.citation: Biol Sex Differ. 2010 Nov 04;1(1):3
references.pmid: 21208465
references.citation: Nature. 1991 May 9;351(6322):117-21
references.pmid: 2030730
references.citation: Chem Biol. 2014 Apr 24;21(4):488-501
references.pmid: 24684905
references.citation: Dev Neurobiol. 2009 Apr;69(5):299-313
references.pmid: 19224561
references.citation: Gen Comp Endocrinol. 2010 Jul 1;167(3):417-21
references.pmid: 19917286
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2011 Dec;160(4):187-93
references.pmid: 21889601
references.citation: BMC Genomics. 2009 Dec 03;10:579
references.pmid: 19958554
references.citation: Gene Expr Patterns. 2002 Dec;2(3-4):359-67
references.pmid: 12617826
references.citation: Nature. 1990 Jul 19;346(6281):240-4
references.pmid: 1695712
references.citation: PLoS One. 2013 Jul 12;8(7):e68452
references.pmid: 23874634
references.citation: Am Nat. 2003 Apr;161(4):676-83
references.pmid: 12776892
references.citation: Mol Biol Evol. 2013 Oct;30(10):2268-85
references.pmid: 23883521
references.citation: PLoS One. 2013 Jul 11;8(7):e68389
references.pmid: 23874606
references.citation: Bioinformatics. 2012 Dec 15;28(24):3326-8
references.pmid: 23060615
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Proc Biol Sci. 2012 Dec 22;279(1749):5014-23
references.pmid: 23075834
references.citation: Mar Biotechnol (NY). 2012 Oct;14(5):591-604
references.pmid: 22544374
references.citation: Gigascience. 2012 Dec 27;1(1):18
references.pmid: 23587118
references.citation: Nature. 2002 May 30;417(6888):559-63
references.pmid: 12037570
references.citation: J Neuroendocrinol. 2007 Aug;19(8):643-55
references.pmid: 17620106
references.citation: Mol Reprod Dev. 2007 Oct;74(10):1239-46
references.pmid: 17342735
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: J Histochem Cytochem. 2009 Oct;57(10):915-22
references.pmid: 19546471
references.citation: Comp Biochem Physiol A Mol Integr Physiol. 2004 Jan;137(1):11-20
references.pmid: 14720586
references.citation: Front Neuroendocrinol. 2010 Apr;31(2):203-16
references.pmid: 20176046
references.citation: Nature. 2009 Sep 10;461(7261):267-71
references.pmid: 19710650
references.citation: PLoS One. 2008 Mar 12;3(3):e1791
references.pmid: 18335061
references.citation: Biol Reprod. 2008 Feb;78(2):200-10
references.pmid: 17959853
references.citation: Hum Mol Genet. 2011 Mar 15;20(6):1132-42
references.pmid: 21196491
references.citation: Curr Biol. 1996 Mar 1;6(3):298-304
references.pmid: 8805249
references.citation: Environ Sci Technol. 2012 Jul 17;46(14):7763-71
references.pmid: 22724546
references.citation: Development. 2012 Dec 1;139(23):4461-72
references.pmid: 23095882
references.citation: PLoS One. 2011 Apr 05;6(4):e18379
references.pmid: 21483681
references.citation: Genesis. 2009 May;47(5):289-99
references.pmid: 19298014
references.citation: PLoS One. 2013 Apr 25;8(4):e56006
references.pmid: 23634199
references.citation: Nat Commun. 2013;4:2771
references.pmid: 24264146
references.citation: Biol Reprod. 2009 Dec;81(6):1073-82
references.pmid: 19605791
references.citation: PLoS One. 2011 Jan 31;6(1):e16599
references.pmid: 21304996
references.citation: BMC Dev Biol. 2011 Dec 01;11:72
references.pmid: 22132805
references.citation: Anim Behav. 2001 Jan;61(1):271-275
references.pmid: 11170716
references.citation: Dev Dyn. 2013 Apr;242(4):360-70
references.pmid: 23335256
references.citation: J Mol Endocrinol. 1999 Oct;23(2):167-76
references.pmid: 10514554
references.citation: Nature. 2008 Jun 12;453(7197):930-4
references.pmid: 18454134
references.citation: Biochem Biophys Res Commun. 2004 Jul 16;320(1):83-9
references.pmid: 15207705
references.citation: J Endocrinol. 2007 Jul;194(1):223-41
references.pmid: 17592036
references.citation: Biochem Biophys Res Commun. 2006 May 26;344(1):353-61
references.pmid: 16630569
references.citation: Anim Genet. 2012 Dec;43(6):753-9
references.pmid: 22497460
references.citation: J Exp Zool A Ecol Genet Physiol. 2007 Nov 1;307(11):625-36
references.pmid: 17726668
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55
references.pmid: 23203987
references.citation: BMC Genomics. 2009 Jul 13;10:308
references.pmid: 19594897
references.citation: BMC Bioinformatics. 2011 Aug 04;12:323
references.pmid: 21816040
references.citation: Biol Reprod. 2000 Dec;63(6):1825-38
references.pmid: 11090455
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: G3 (Bethesda). 2011 Jun 1;1(1):3-9
references.pmid: 21949597
references.citation: Mol Reprod Dev. 2012 Jan;79(1):51-63
references.pmid: 22125114
references.citation: Biol Reprod. 2012 Feb 14;86(2):41
references.pmid: 22034528
references.citation: FEBS J. 2011 Apr;278(7):1010-9
references.pmid: 21281449
references.citation: Cell Mol Life Sci. 2010 Jan;67(1):123-33
references.pmid: 19898775
references.citation: Bioessays. 2003 Jan;25(1):1-4
references.pmid: 12508274
references.citation: Cytogenet Genome Res. 2003;101(3-4):309-13
references.pmid: 14685000
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: BMC Dev Biol. 2012 Dec 07;12:36
references.pmid: 23217106
references.citation: BMC Bioinformatics. 2013 Mar 09;14:91
references.pmid: 23497356
references.citation: Dev Biol. 2005 Nov 15;287(2):361-77
references.pmid: 16214126
references.citation: Biol Reprod. 2010 Sep;83(3):443-53
references.pmid: 20505169
references.citation: Bioinformatics. 2011 Jun 15;27(12):1691-2
references.pmid: 21493652
references.citation: Bioinformatics. 2012 Apr 15;28(8):1086-92
references.pmid: 22368243
references.citation: Nat Rev Genet. 2012 Feb 07;13(3):163-74
references.pmid: 22310892
references.citation: Genetics. 2009 Dec;183(4):1443-52
references.pmid: 19786621
references.citation: Mol Reprod Dev. 2012 Aug;79(8):504-16
references.pmid: 22618959
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2955-9
references.pmid: 22323585
references.citation: Endocrinology. 2005 Aug;146(8):3558-66
references.pmid: 15878962
references.citation: Biol Reprod. 2008 Dec;79(6):1111-20
references.pmid: 18667752
references.citation: Bioinformatics. 2001 Sep;17(9):847-8
references.pmid: 11590104
references.citation: Curr Biol. 2012 Aug 7;22(15):1423-8
references.pmid: 22727696
references.citation: Gene Expr Patterns. 2007 Jan;7(1-2):82-92
references.pmid: 16844427
references.citation: Adv Exp Med Biol. 2009;665:207-26
references.pmid: 20429427
references.citation: Integr Comp Biol. 2013 Oct;53(4):736-54
references.pmid: 23817661
references.citation: Reproduction. 2009 Aug;138(2):329-39
references.pmid: 19433502
references.citation: Genome Biol. 2013;14(9):R95
references.pmid: 24020486
references.citation: Gen Comp Endocrinol. 2011 Jan 15;170(2):346-55
references.pmid: 20955710
references.citation: Bioinformatics. 2009 Mar 15;25(6):824-6
references.pmid: 19181685
references.citation: PLoS One. 2013 May 03;8(5):e63604
references.pmid: 23658843
references.citation: Curr Top Dev Biol. 2013;102:327-56
references.pmid: 23287039
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2013 Jun;165(2):125-37
references.pmid: 23507626
references.citation: Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11778-83
references.pmid: 12193652
references.citation: Int J Med Sci. 2013 Jul 05;10(9):1121-34
references.pmid: 23869188
references.citation: Mol Cell Endocrinol. 2014 Feb 15;382(2):915-25
references.pmid: 24246780
references.citation: Mol Biol Evol. 2013 Oct;30(10):2328-46
references.pmid: 23883523
references.citation: Nat Protoc. 2013 Aug;8(8):1494-512
references.pmid: 23845962
references.citation: BMC Genomics. 2013 Aug 20;14:566
references.pmid: 23957753
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Gen Comp Endocrinol. 2010 Feb 1;165(3):352-66
references.pmid: 19289125
references.citation: PLoS One. 2012;7(7):e40465
references.pmid: 22792339
references.citation: PLoS One. 2013;8(3):e58815
references.pmid: 23555596
references.citation: PLoS Genet. 2012;8(7):e1002798
references.pmid: 22807687
references.citation: Biochem Biophys Res Commun. 2002 Sep 27;297(3):632-40
references.pmid: 12270141
references.citation: Gen Comp Endocrinol. 2011 Dec 1;174(3):259-68
references.pmid: 21906596
references.citation: Mol Cell Proteomics. 2009 Dec;8(12):2624-41
references.pmid: 19617587
references.citation: Reprod Biol Endocrinol. 2007 May 30;5:19
references.pmid: 17537257
references.citation: Curr Biol. 2004 Aug 24;14(16):1416-24
references.pmid: 15324658
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Science. 1998 Sep 25;281(5385):1990-4
references.pmid: 9748152
references.citation: Fish Physiol Biochem. 2013 Feb;39(1):33-8
references.pmid: 22411079