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Genome assembly and annotation of a Drosophila simulans strain from Madagascar
Drosophila simulans is a close relative of the genetic model D. melanogaster. Its worldwide distribution in combination with the absence of segregating chromosomal inversions makes this species an increasingly attractive model to study the molecular signatures of adaptation in natural and experiment...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Blackwell Publishing Ltd
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344813/ https://www.ncbi.nlm.nih.gov/pubmed/24961367 http://dx.doi.org/10.1111/1755-0998.12297 |
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author | PALMIERI, NICOLA NOLTE, VIOLA CHEN, JUN SCHLÖTTERER, CHRISTIAN |
author_facet | PALMIERI, NICOLA NOLTE, VIOLA CHEN, JUN SCHLÖTTERER, CHRISTIAN |
author_sort | PALMIERI, NICOLA |
collection | PubMed |
description | Drosophila simulans is a close relative of the genetic model D. melanogaster. Its worldwide distribution in combination with the absence of segregating chromosomal inversions makes this species an increasingly attractive model to study the molecular signatures of adaptation in natural and experimental populations. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions. |
format | Online Article Text |
id | pubmed-4344813 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Blackwell Publishing Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-43448132015-03-04 Genome assembly and annotation of a Drosophila simulans strain from Madagascar PALMIERI, NICOLA NOLTE, VIOLA CHEN, JUN SCHLÖTTERER, CHRISTIAN Mol Ecol Resour Resource Articles Drosophila simulans is a close relative of the genetic model D. melanogaster. Its worldwide distribution in combination with the absence of segregating chromosomal inversions makes this species an increasingly attractive model to study the molecular signatures of adaptation in natural and experimental populations. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions. Blackwell Publishing Ltd 2015-03 2014-07-14 /pmc/articles/PMC4344813/ /pubmed/24961367 http://dx.doi.org/10.1111/1755-0998.12297 Text en © 2014 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd. http://creativecommons.org/licenses/by/3.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Resource Articles PALMIERI, NICOLA NOLTE, VIOLA CHEN, JUN SCHLÖTTERER, CHRISTIAN Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title | Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title_full | Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title_fullStr | Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title_full_unstemmed | Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title_short | Genome assembly and annotation of a Drosophila simulans strain from Madagascar |
title_sort | genome assembly and annotation of a drosophila simulans strain from madagascar |
topic | Resource Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344813/ https://www.ncbi.nlm.nih.gov/pubmed/24961367 http://dx.doi.org/10.1111/1755-0998.12297 |
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