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Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
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 stil...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630058/ https://www.ncbi.nlm.nih.gov/pubmed/23552491 http://dx.doi.org/10.1186/1759-8753-4-13 |
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author | Negre, Bárbara Simpson, Pat |
author_facet | Negre, Bárbara Simpson, Pat |
author_sort | Negre, Bárbara |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3630058 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36300582013-04-19 Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina Negre, Bárbara Simpson, Pat Mob DNA Research 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. BioMed Central 2013-04-03 /pmc/articles/PMC3630058/ /pubmed/23552491 http://dx.doi.org/10.1186/1759-8753-4-13 Text en Copyright © 2013 Negre and Simpson; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Negre, Bárbara Simpson, Pat Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title | Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title_full | Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title_fullStr | Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title_full_unstemmed | Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title_short | Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina |
title_sort | diversity of transposable elements and repeats in a 600 kb region of the fly calliphora vicina |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630058/ https://www.ncbi.nlm.nih.gov/pubmed/23552491 http://dx.doi.org/10.1186/1759-8753-4-13 |
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