Abstract
BackgroundTransposable 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.ResultsHere, 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.ConclusionsThis 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.
Highlights
IntroductionTransposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools)
Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications and applications
This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution adds to our knowledge about TE evolution but will help in the annotation of repeats on Dipteran whole genome sequences
Summary
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 represent a major challenge for the assembly and annotation of genomic sequences. They are still largely unknown in non-model species. 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 and other repeats pose a big challenge for the assembly and annotation of genomic sequences. Many programs have been developed for the detection of TEs, most are difficult to use and their
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