title: Genomic resources for multiple species in the Drosophila ananassae species group.
abstract: The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.
authors: Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA. sasignor@ucdavis.edu
authors: Sarah
authors: S
authors: Signor
authors: Thaddeus
authors: T
authors: Seher
authors: Artyom
authors: A
authors: Kopp
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D059006:Chromosomes, Insect; D003433:Crosses, Genetic; D004330:Drosophila / Q000235:genetics*; D015723:Gene Library; D005819:Genetic Markers; D016678:Genome; D006824:Hybridization, Genetic; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Drosophila; ananassae; genotyping; linkage map; transcriptome
references: Nat Methods. 2010 Nov;7(11):909-12
references: 20935650
references: G3 (Bethesda). 2012 Feb;2(2):287-97
references: 22384407
references: Heredity (Edinb). 2009 Nov;103(5):416-24
references: 19654611
references: Genetics. 1941 Sep;26(5):517-41
references: 17247021
references: Insect Mol Biol. 2012 Feb;21(1):89-95
references: 22136651
references: Heredity (Edinb). 2008 Feb;100(2):158-70
references: 17314923
references: Genet Res. 2005 Feb;85(1):23-46
references: 16089034
references: J Evol Biol. 2011 Sep;24(9):1879-86
references: 21635604
references: Genome Res. 2011 Apr;21(4):610-7
references: 21233398
references: Genetics. 2008 Jul;179(3):1601-55
references: 18622037
references: J Hered. 2002 Jan-Feb;93(1):77-8
references: 12011185
references: BMC Bioinformatics. 2009 Dec 15;10:421
references: 20003500
references: Genetics. 2008 Jul;179(3):1657-80
references: 18622036
references: Mol Ecol Resour. 2011 Mar;11 Suppl 1:81-92
references: 21429165
references: Genome Res. 2000 Jul;10(7):967-81
references: 10899146
references: Genetics. 2010 Nov;186(3):997-1012
references: 20823339
references: Bioinformatics. 2010 Mar 1;26(5):589-95
references: 20080505
references: J Microbiol Methods. 2011 Sep;86(3):368-75
references: 21749903
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D706-14
references: 22127867
references: Evolution. 2010 Jan;64(1):253-60
references: 19686263
references: Bioinformatics. 2003 May 1;19(7):889-90
references: 12724300
references: Heredity (Edinb). 2010 Aug;105(2):213-9
references: 19953119
references: Mamm Genome. 2010 Dec;21(11-12):592-8
references: 21057797
references: Genetics. 2011 Aug;188(4):799-808
references: 21828280
references: Genetics. 2011 Dec;189(4):1203-9
references: 21940681
references: Mol Ecol. 2008 Jun;17(11):2706-21
references: 18466237
references: Bioessays. 1994 Apr;16(4):269-75
references: 8031304
references: Nat Rev Genet. 2011 Jun 17;12(7):499-510
references: 21681211
references: Fly (Austin). 2009 Apr-Jun;3(2):157-69
references: 19377294
references: Bioinformatics. 2008 Mar 1;24(5):713-4
references: 18227114
references: Trends Genet. 2000 Oct;16(10):461-8
references: 11050333
references: Genetica. 2011 Feb;139(2):273-9
references: 21234646
references: BMC Genet. 2004 May 26;5:12
references: 15163351
references: Nature. 2007 Nov 8;450(7167):203-18
references: 17994087
references: Evol Dev. 2002 Jul-Aug;4(4):278-91
references: 12168620
references: BMC Plant Biol. 2011 Oct 28;11:147
references: 22035129
references: Nat Rev Genet. 2009 Jan;10(1):57-63
references: 19015660
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references: 18948289
references: Bioinformatics. 2011 Aug 15;27(16):2187-93
references: 21712251
references: Genetics. 2007 Aug;176(4):2489-500
references: 17603096
references: Heredity (Edinb). 2011 Jul;107(1):22-9
references: 21157499
references: Genome Res. 2005 Jan;15(1):1-18
references: 15632085
references: BMC Genomics. 2010 Nov 24;11:663
references: 21106091
references: Genome. 2005 Jun;48(3):487-502
references: 16121245
references: BMC Genomics. 2010 Mar 16;11:180
references: 20233449
references: Chromosoma. 1971;34(2):206-29
references: 5096943
references: Evolution. 2011 Jul;65(7):1969-78
references: 21729052
references: Indian J Exp Biol. 2001 Sep;39(9):835-44
references: 11831362
references: PLoS One. 2008;3(10):e3376
references: 18852878
references: J Evol Biol. 2011 Dec;24(12):2678-86
references: 21954914
references: Science. 2008 Apr 25;320(5875):495-7
references: 18436781
references: Bioinformatics. 2009 Sep 1;25(17):2283-5
references: 19542151
references: Science. 2000 Mar 24;287(5461):2185-95
references: 10731132
references: Nature. 2001 Feb 15;409(6822):860-921
references: 11237011
references: BMC Evol Biol. 2009 Dec 16;9:291
references: 20015359
references: PLoS One. 2011 Apr 13;6(4):e18561
references: 21541009
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: Nucleic Acids Res. 2004 Feb 18;32(3):e37
references: 14973331
references: Genome Res. 2009 Jun;19(6):1117-23
references: 19251739
references: Mol Ecol. 2010 Mar;19 Suppl 1:115-31
references: 20331775
references: Genetics. 2012 Dec;192(4):1465-75
references: 23086218