Transposable elements (TEs) are a common feature in eukaryotic genomes and constitute a major player in many of the processes that shape the genome and control gene expression [1, 2]. TEs can occupy a significant but highly variable portion of the genome. For example, at least 46% of the initial sequence of the human genome was recognized as TEs, and this percentage is probably higher than 50% when other repeats are considered . Amongst species of Diptera sequenced to date the repeat content of euchromatic regions varies from only 6% in Drosophila melanogaster to 16% in Anopheles gambiae, 28% in Culex quinquefasciatus and 47% in Aedes aegypti. TEs and other repeats pose a big challenge for the assembly and annotation of genomic sequences. Although many programs have been developed for the detection of TEs, most are difficult to use and their performance has not been properly tested . They mostly rely on similarity to annotated elements or on the detection of known structures. The availability of well-annotated elements is thus of great help for their automatic detection and annotation.
Detailed description of TEs is not only important for genome annotation but also essential for understanding genome structure, function and evolution. The presence of TEs can affect gene structure and gene expression in several ways: from local effects on the expression of adjacent genes, to global effects such as the generation of large chromosome rearrangements or transpositions [2, 9]. TEs are also important contributors to evolutionary adaptation . Furthermore they contain historical information about the genome, and can be used as a sort of paleontological record. They provide a tool with which to solve evolutionary relationships and classification of species [11–14]. Moreover, TEs have a direct application for transgenesis where they can be used as insertion vectors. Knowledge of the TE repertoire of a target species has important implications for vector choice, as it will influence the stability of the transgenes. These methods are not only valuable research tools but are also being developed for the control of pest species in the wild .
TEs are divided into two main classes according to their structure and mechanism of transposition . Class I elements, also called retrotransposons, transpose by reverse transcription of an RNA intermediate (DNA-RNA-DNA) mediated by a retrotranscriptase, whereas Class II elements transpose directly from DNA to DNA. Within each of these classes, TEs are further subdivided mainly on the basis of the structural features of their sequences [17, 18]. Class I elements are divided into two main types: with or without Long Terminal Repeats (LTR elements and non-LTR elements), such as LINEs and SINEs. Class II elements include cut-and-paste DNA transposons, rolling-circle DNA transposons (Helitrons) and self-synthesizing DNA transposons (Polintons). Cut-and-paste DNA transposons are characterized by the presence of Terminal Inverted Repeats (TIRs) flanking a transposase that catalyses the transposition reaction. Helitrons have been classified as Class II-DNA transposons that use a “rolling circle” (RC) mode of transposition .
The Calliphoridae is a monophyletic family of calyptrate Muscomorpha (Diptera). These flies are of economic importance as a cause of myiasis in humans and animals, and as vectors of pathogens causing dysentery and other diseases. The larvae of most species are scavengers of carrion and dung, and fulfil an important ecological function in the decomposition of animal remains. They are among the first colonizers of cadavers, making them particularly useful for forensic entomology, predominantly to establish a minimum time since death, or minimum post-mortem interval . This method usually relies on morphological identification of samples collected on corpses. Distinguishing between closely related taxa, such as Calliphora vicina and Calliphora vomitoria, can be a difficult process with major implications for post-mortem interval estimation. Mitochondrial sequences, like COI and COII, have been used for species identification but in some cases an overlap between intra- and inter-specific variability renders this method unreliable . Measures to develop a TE-based simple and efficient marker system for the identification of forensically important carrion flies are currently being developed . However, the retrotransposon landscape of carrion fly genomes remains largely unknown.
Here we provide an inventory and classification of the TEs and other repeats found in 6 BAC clones covering most of the Achaete-Scute Complex of C. vicina. These sequences include the genes achaete (ac), scute (sc) and lethal of scute (l’sc) which are highly regulated and surrounded by large regulatory regions. It is a 600 kb euchromatic region of the 750 Mb C. vicina genome. We have identified 318 insertions classified as 75 different repeats; 42 of which are TEs and 33 are unclassified repeats. Elements which are complete or present at high copy number are described in some detail. We also discuss probable cases of horizontal transfer.