Open Access Highly Accessed Research article

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

Dietmar Schwarz15*, Hugh M Robertson1, Jeffrey L Feder2, Kranthi Varala3, Matthew E Hudson3, Gregory J Ragland4, Daniel A Hahn4 and Stewart H Berlocher1

Author Affiliations

1 Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S. Goodwin Ave, Urbana, Illinois, 61801, USA

2 Department of Biological Sciences, PO Box 369, Galvin Life Science Center, University of Notre Dame, Notre Dame, Indiana, 46556-0369, USA

3 Department of Crop Sciences, University of Illinois, AW-101 Turner Hall, Urbana, Illinois, 61801, USA

4 Department of Entomology and Nematology, University of Florida, PO Box 110620, Gainesville, Florida, 32611-0620, USA

5 Department of Biology, Western Washington University, BI 315 MS9160, Bellingham, Washington, 98225, USA

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BMC Genomics 2009, 10:633  doi:10.1186/1471-2164-10-633

Published: 27 December 2009

Additional files

Additional file 1:

Supplemental table. Table of sequencing scheme and summary statistics for titration and bulk runs.

Format: DOC Size: 102KB Download file

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Additional file 2:

Descriptive figures of contig lengths and coverage. 2a. Distribution of contig lengths. 2b. Coverage (number of reads per contig) by contig length.

Format: DOC Size: 291KB Download file

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Additional file 3:

Table of candidate ESTs for diapause regulation and emergence timing. Contigs and reads matching the same D. melanogaster locus map to different regions of the D. melanogaster gene. Match is the D. melanogaster locus name for the closest match, CG is the Celera Genome number of the match, aa is the number of amino acids in the single read or contig, %I is the percent aa match between the R. pomonella and D. melanogaster homologous proteins, bp is the base pair length of the single read or contig (number of sequences contributing to contig), Read/Contig is the R. pomonella ID in our data base.

Format: DOCX Size: 46KB Download file

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Additional file 4:

Table of contigs containing SNPs that differed in frequency between the two host races. Contig is the R. pomonella contig number followed by the TSA accession number. CG is the D. melanogaster Celera Genome number of the locus with the closest match and Annotation is the D. melanogaster locus name where known.

Format: DOCX Size: 37KB Download file

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Additional file 5:

Table of listing synonomous/nonsynonomous changes in contigs containing SNPs that differed in frequency between the two host races. For those contigs where an open reading frame could be clearly identified, we determined whether SNPs would affect the amino acid sequence of the protein product. Contig is the R. pomonella contig number followed by the TSA accession number. CG is the D. melanogaster Celera Genome number of the locus with the closest match and Annotation is the D. melanogaster locus name where known. Position denotes the nucleotide location within the contig and synonymous? denotes whether the alternative forms of the SNP specify alternative amino acids. We also define the consensus amino acid, the alternative amino acid, the consensus codon and whether the SNP site is within the local BLAST alignment of our data with the hit to the identified D. melanogaster locus.

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Additional file 6:

Table describing microsatellite discovery. 6a. Summary of potential microsatellite loci identified. 6b. List of contigs and singletons containing potential microsatellite loci including repeat type and length.

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Additional file 7:

Table of transcript gain in the lineage leading to the Schizophora since the last common ancestor of mosquitoes, Rhagoletis, and Drosophila. D. melanogaster annotation denotes the Celera Genome number of the locus with the closest match and locus name where known. Contig is the R. pomonella contig number followed by the TSA accession number.

Format: DOCX Size: 12KB Download file

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