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Open Access Research

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

Bárbara Negre12* and Pat Simpson1

Author Affiliations

1 Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK

2 Current address: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), and Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, 08003, Spain

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Mobile DNA 2013, 4:13  doi:10.1186/1759-8753-4-13

Published: 3 April 2013

Abstract

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.

Keywords:
Calliphora vicina; Diptera; Helitrons; Horizontal transfer; Repeats; Retrotransposons; Transposable elements; Transposons