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Background  Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications ( e.g. , in evolution) and applications ( e.g. , as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species.    Results  Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly  Calliphora vicina  (Diptera: Calliphoridae) which contains most of the  achaete-scute  gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the  Drosophila  genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats.    Conclusions  This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences.

Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina