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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 633.
Published online Dec 27, 2009. doi:  10.1186/1471-2164-10-633
PMCID: PMC2807884
Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella
Dietmar Schwarz,corresponding author1,5 Hugh M Robertson,1 Jeffrey L Feder,2 Kranthi Varala,3 Matthew E Hudson,3 Gregory J Ragland,4 Daniel A Hahn,4 and Stewart H Berlocher1
1Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S. Goodwin Ave, Urbana, Illinois, 61801, USA
2Department of Biological Sciences, PO Box 369, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana, 46556-0369, USA
3Department of Crop Sciences, University of Illinois, AW-101 Turner Hall, Urbana, Illinois, 61801, USA
4Department of Entomology and Nematology, University of Florida, PO Box 110620, Gainesville, Florida, 32611-0620, USA
5Department of Biology, Western Washington University, BI 315 MS9160, Bellingham, Washington, 98225, USA
corresponding authorCorresponding author.
Dietmar Schwarz: Dietmar.Schwarz/at/wwu.edu; Hugh M Robertson: hughrobe/at/life.uiuc.edu; Jeffrey L Feder: jfeder/at/nd.edu; Kranthi Varala: kvarala2/at/uiuc.edu; Matthew E Hudson: mhudson/at/illinois.edu; Gregory J Ragland: gragland/at/ufl.edu; Daniel A Hahn: dahahn/at/ufl.edu; Stewart H Berlocher: stewartb/at/life.uiuc.edu
Received August 14, 2009; Accepted December 27, 2009.
Abstract
Background
The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed sequence tag (EST) study of a candidate for ecological sympatric speciation, the apple maggot Rhagoletis pomonella, using massively parallel pyrosequencing on the Roche 454-FLX platform. To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies.
Results
We obtained 239,531 sequences which assembled into 24,373 contigs. A total of 6810 unique protein coding genes were identified among the contigs and long singletons, corresponding to 48% of all known Drosophila melanogaster protein-coding genes. Their distribution across GO classes suggests that we have obtained a representative sample of the transcriptome. Among these sequences are many candidates for potential R. pomonella "speciation genes" (or "barrier genes") such as those controlling chemosensory and life-history timing processes. Furthermore, we identified important marker loci including more than 40,000 single nucleotide polymorphisms (SNPs) and over 100 microsatellites. An initial search for SNPs at which the apple and hawthorn host races differ suggested at least 75 loci warranting further work. We also determined that developmental expression differences remained even after normalization; transcripts expected to show different expression levels between larvae and pupae in D. melanogaster also did so in R. pomonella. Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora.
Conclusions
These data provide a much needed resource for exploring mechanisms of divergence in this important model for sympatric ecological speciation. Our description of ESTs from a substantial portion of the R. pomonella transcriptome will facilitate future functional studies of candidate genes for olfaction and diapause-related life history timing, and will enable large scale expression studies. Similarly, the identification of new SNP and microsatellite markers will facilitate future population and quantitative genetic studies of divergence between the apple and hawthorn-infesting host races.
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