title: Massively parallel resequencing of the isogenic Drosophila melanogaster strain w(1118); iso-2; iso-3 identifies hotspots for mutations in sensory perception genes.
abstract: We used the Illumina reversible-short sequencing technology to obtain 17-fold average depth (s.d. approximately 8) of approximately 94% of the euchromatic genome and approximately 1-5% of the heterochromatin sequence of the Drosophila melanogaster isogenic strain w(1118); iso-2; iso-3. We show that this strain has a approximately 9 kb deletion that uncovers the first exon of the white (w) gene, approximately 4 kb of downstream promoter sequences, and most of the first intron, thus demonstrating that whole-genome sequencing can be used for mutation characterization. We chose this strain because there are thousands of transposon insertion lines and hundreds of isogenic deficiency lines available with this genetic background, such as the Exelixis, Inc., and the DrosDEL collections. We compared our sequence to Release 5 of the finished reference genome sequence which was made from the isogenic strain y(1); cn(1) bw(1) sp(1) and identified 356,614 candidate SNPs in the approximately 117 Mb unique sequence genome, which represents a substitution rate of approximately 1/305 nucleotides ( approximately 0.30%). The distribution of SNPs is not uniform, but rather there is a approximately 2-fold increase in SNPs on the autosome arms compared with the X chromosome and a approximately 7-fold increase when compared to the small 4(th) chromosome. This is consistent with previous analyses that demonstrated a correlation between recombination frequency and SNP frequency. An unexpected finding was a SNP hotpot in a approximately 20 Mb central region of the 4(th) chromosome, which might indicate higher than expected recombination frequency in this region of this chromosome. Interestingly, genes involved in sensory perception are enriched in SNP hotspots and genes encoding developmental genes are enriched in SNP coldspots, which suggests that recombination frequencies might be proportional to the evolutionary selection coefficient. There are currently 12 Drosophila species sequenced, and this represents one of many isogenic Drosophila melanogaster genome sequences that are in progress. Because of the dramatic increase in power in using isogenic lines rather than outbred individuals, the SNP information should be valuable as a test bed for understanding genotype-by-environment interactions in human population studies.
authors.affiliation: The Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Platts
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Land
authors.forename: Lang
authors.initials: L
authors.lastname: Chen
authors.forename: Grier P
authors.initials: GP
authors.lastname: Page
authors.forename: Parsa
authors.initials: P
authors.lastname: Rasouli
authors.forename: Luan
authors.initials: L
authors.lastname: Wang
authors.forename: Xiangyi
authors.initials: X
authors.lastname: Lu
authors.forename: Douglas M
authors.initials: DM
authors.lastname: Ruden
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002875:Chromosomes; D004331:Drosophila melanogaster / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D018035:Receptors, Odorant / Q000737:chemistry / Q000235:genetics; D011984:Sensory Receptor Cells / Q000378:metabolism
chemical_list: C529204:Obp57d protein, Drosophila; D018035:Receptors, Odorant
references.citation: Nat Methods. 2008 Feb;5(2):183-8
references.pmid: 18204455
references.citation: Nat Genet. 2000 Oct;26(2):221-4
references.pmid: 11017082
references.citation: Nat Methods. 2007 Oct;4(10):839-41
references.pmid: 17873888
references.citation: Genetics. 2007 Sep;177(1):615-29
references.pmid: 17720900
references.citation: PLoS Biol. 2006 Mar;4(3):e72
references.pmid: 16494531
references.citation: Nat Genet. 2003 Aug;34(4):429-33
references.pmid: 12881721
references.citation: Nature. 2008 Nov 6;456(7218):53-9
references.pmid: 18987734
references.citation: Methods Mol Biol. 2007;372:33-49
references.pmid: 18314716
references.citation: Nature. 2004 Oct 21;431(7011):931-45
references.pmid: 15496913
references.citation: Mol Biol Evol. 2003 Oct;20(10):1705-9
references.pmid: 12832636
references.citation: Radiat Res. 2008 Dec;170(6):784-93
references.pmid: 19138034
references.citation: Science. 2000 Mar 24;287(5461):2216-8
references.pmid: 10731135
references.citation: Science. 2009 Jan 16;323(5912):342
references.pmid: 19150830
references.citation: Nature. 2005 Oct 27;437(7063):1299-320
references.pmid: 16255080
references.citation: Genome Biol. 2003;4(5):P3
references.pmid: 12734009
references.citation: Nature. 1992 Apr 9;356(6369):519-20
references.pmid: 1560824
references.citation: Front Neuroendocrinol. 2008 Jun;29(3):428-44
references.pmid: 18295320
references.citation: Nat Genet. 2004 Mar;36(3):288-92
references.pmid: 14981519
references.citation: Genet Res. 1996 Oct;68(2):131-49
references.pmid: 8940902
references.citation: Gene. 2002 Sep 4;297(1-2):69-78
references.pmid: 12384287
references.citation: Nat Genet. 2004 Mar;36(3):283-7
references.pmid: 14981521
references.citation: Nature. 2007 Nov 8;450(7167):203-18
references.pmid: 17994087
references.citation: Nature. 2008 Nov 6;456(7218):60-5
references.pmid: 18987735
references.citation: Nature. 1988 Sep 8;335(6186):167-70
references.pmid: 3412472
references.citation: Genome Biol. 2003;4(10):R70
references.pmid: 14519205
references.citation: Science. 2000 Mar 24;287(5461):2185-95
references.pmid: 10731132
references.citation: Am J Hum Genet. 2003 Jun;72(6):1527-35
references.pmid: 12740762
references.citation: Genome Res. 2001 Jun;11(6):1100-13
references.pmid: 11381036
references.citation: Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):10860-5
references.pmid: 12960394
references.citation: Nat Methods. 2008 Oct;5(10):865-7
references.pmid: 18677319
references.citation: Nat Genet. 2007 Feb;39(2):144-5
references.pmid: 17262025
references.citation: BMC Genomics. 2008 May 29;9:256
references.pmid: 18510772
references.citation: PLoS Biol. 2005 Jun;3(6):e170
references.pmid: 15869325
references.citation: Science. 2000 Mar 24;287(5461):2196-204
references.pmid: 10731133
references.citation: Science. 2003 Dec 12;302(5652):1960-3
references.pmid: 14671302