Diversity of Transposable Elements and Repeats in a 600 Kb Region of the Fly Calliphora Vicina

Overview

Journal Mob DNA

Publisher Biomed Central

Specialty Genetics

Date 2013 Apr 5

PMID 23552491

Citations 3

Authors

Barbara Negre

Pat Simpson

Affiliations

Soon will be listed here.

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.

Citing Articles

The genomes of a monogenic fly: views of primitive sex chromosomes.

Andere A, Pimsler M, Tarone A, Picard C Sci Rep. 2020; 10(1):15728.

PMID: 32978490 PMC: 7519133. DOI: 10.1038/s41598-020-72880-0.

The achaete-scute complex in Diptera: patterns of noncoding sequence evolution.

Negre B, Simpson P J Evol Biol. 2015; 28(10):1770-81.

PMID: 26134680 PMC: 4832353. DOI: 10.1111/jeb.12687.

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons).

Thomas J, Vadnagara K, Pritham E Mob DNA. 2014; 5:18.

PMID: 24959209 PMC: 4067079. DOI: 10.1186/1759-8753-5-18.

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