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Background  To have an insight into the  Mayetiola destructor  (Hessian fly) genome, we performed an  in silico  comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases.    Results  Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene  vH13 . These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study.  In silico  gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly,  Drosophila melanogaster , and the malaria mosquito,  Anopheles gambiae , and to infer evolutionary relationships.    Conclusion  This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.

Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13