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Background  With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly  Heliconius erato  provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic  Heliconius melpomene ,  H. erato  also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of  H. erato  and  H. melpomene . To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in  Heliconius .    Results  Scoring AFLP polymorphisms in  H. erato  broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes:  D  and  Cr , which were then used to screen  H. erato  BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the  D-  and  Cr -linked  H. erato  BAC sequences and on the  Yb -linked  H. melpomene  BAC sequence. A comparative analysis between homologous regions of  H. erato  ( Cr -linked BAC) and  H. melpomene  ( Yb -linked BAC) revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from  H. erato  and  H. melpomene  respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between  Heliconius  and the moth  Bombyx mori , suggesting that lepidopteran genome architecture may be conserved over very long evolutionary time scales.    Conclusion  Here we have demonstrated the tractability of progressing from a genetic linkage map to genomic sequence data in  Heliconius  butterflies. We have also shown that fine-scale gene order is highly conserved between distantly related  Heliconius  species, and also between  Heliconius  and  B. mori . Together, these findings suggest that genome structure in macrolepidoptera might be very conserved, and show that mapping and positional cloning efforts in different lepidopteran species can be reciprocally informative.

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies