title: Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens).
abstract: Modern pyrosequencing has the potential to uncover many interesting aspects of genome evolution, even in lineages where genomic resources are scarce. In particular, 454 pyrosequencing of nonmodel species has been used to characterize expressed sequence tags, xenobiotics, gene ontologies, and relative levels of gene expression. Herein, we use pyrosequencing to study the evolution of genes expressed in the gonads of a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454 pyrosequencing of transcribed genes, we produced more than 125 MB of sequence data from 473,577 high-quality sequencing reads. Sequences that passed stringent quality control thresholds were assembled into 12,791 male contigs and 32,629 female contigs. Average depth of coverage was 4.2 x for the male assembly and 5.5x for the female assembly. Analytical rarefaction indicates that our assemblies include most of the genes expressed in lake sturgeon gonads. Over 86,700 sequencing reads were assigned gene ontologies, many to general housekeeping genes like protein, RNA, and ion binding genes. We searched specifically for sex determining genes and documented significant sex differences in the expression of two genes involved in animal sex determination, DMRT1 and TRA-1. DMRT1 is the master sex determining gene in birds and in medaka (Oryzias latipes) whereas TRA-1 helps direct sexual differentiation in nematodes. We also searched the lake sturgeon assembly for evidence of xenobiotic organisms that may exist as endosymbionts. Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome.
authors.affiliation: Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47906, USA. mchale@purdue.edu
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Hale
authors.forename: James R
authors.initials: JR
authors.lastname: Jackson
authors.forename: J Andrew
authors.initials: JA
authors.lastname: Dewoody
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D005260:Female; D029941:Fish Proteins / Q000235:genetics*; D005399:Fishes / Q000235:genetics*; D015723:Gene Library; D022761:Gene Transfer, Horizontal; D006066:Gonads / Q000378:metabolism*; D008297:Male; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes / Q000235:genetics*; D012733:Sex Differentiation / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: C110547:DMRT1 protein; D018076:DNA, Complementary; D029941:Fish Proteins; D014157:Transcription Factors
references.citation: BMC Genomics. 2009 Apr 29;10:203
references.pmid: 19402907
references.citation: BMC Genomics. 2008 Jun 30;9:312
references.pmid: 18590545
references.citation: Nature. 1990 Jul 19;346(6281):240-4
references.pmid: 1695712
references.citation: Nature. 2008 Nov 20;456(7220):387-90
references.pmid: 19020620
references.citation: Nature. 2009 Sep 10;461(7261):267-71
references.pmid: 19710650
references.citation: Sex Dev. 2009;3(2-3):152-63
references.pmid: 19684459
references.citation: BMC Genomics. 2006 Oct 26;7:275
references.pmid: 17067373
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Gen Comp Endocrinol. 2008 May 15;157(1):75-85
references.pmid: 18452918
references.citation: Biotechniques. 2001 Apr;30(4):892-7
references.pmid: 11314272
references.citation: BMC Genomics. 2006 Oct 24;7:272
references.pmid: 17062153
references.citation: Nat Genet. 2004 Aug;36(8):786-7
references.pmid: 15284843
references.citation: Genetics. 2001 Jul;158(3):1203-15
references.pmid: 11454768
references.citation: Curr Biol. 2004 Sep 21;14(18):1664-9
references.pmid: 15380069
references.citation: Nature. 2002 May 30;417(6888):559-63
references.pmid: 12037570
references.citation: Genome Res. 2008 Jan;18(1):172-7
references.pmid: 18032722
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11349-54
references.pmid: 16061812
references.citation: Genome. 2005 Apr;48(2):181-6
references.pmid: 15838539
references.citation: Plant J. 2007 Sep;51(5):910-8
references.pmid: 17662031
references.citation: Gene. 2009 Apr 1;434(1-2):16-28
references.pmid: 18590946
references.citation: Mol Ecol Resour. 2008 Jan;8(1):3-17
references.pmid: 21585713
references.citation: Genome Biol. 2007;8(7):R143
references.pmid: 17659080
references.citation: Mol Ecol. 2009 May;18(9):2022-38
references.pmid: 19317847
references.citation: Plant Physiol. 2007 May;144(1):32-42
references.pmid: 17351049
references.citation: Genome Res. 2003 Sep;13(9):2164-70
references.pmid: 12952883
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: BMC Genomics. 2008 Nov 15;9:542
references.pmid: 19014603
references.citation: Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11778-83
references.pmid: 12193652
references.citation: Sex Dev. 2007;1(1):2-11
references.pmid: 18391511
references.citation: BMC Plant Biol. 2006 Aug 25;6:17
references.pmid: 16934154
references.citation: Clin Microbiol Rev. 2004 Oct;17(4):794-803, table of contents
references.pmid: 15489349
references.citation: Mol Ecol. 2008 Apr;17(7):1636-47
references.pmid: 18266620
references.citation: Trends Parasitol. 2001 Jul;17(7):320-4
references.pmid: 11423374