Genome assembly and annotation of a Drosophila simulans strain from Madagascar
Article first published online: 13 JUL 2014
© 2014 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.
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.
Molecular Ecology Resources
Volume 15, Issue 2, pages 372–381, March 2015
How to Cite
Palmieri, N., Nolte, V., Chen, J. and Schlötterer, C. (2015), Genome assembly and annotation of a Drosophila simulans strain from Madagascar. Molecular Ecology Resources, 15: 372–381. doi: 10.1111/1755-0998.12297
- Issue published online: 11 FEB 2015
- Article first published online: 13 JUL 2014
- Accepted manuscript online: 24 JUN 2014 09:52AM EST
- Manuscript Revised: 20 JUN 2014
- Manuscript Accepted: 20 JUN 2014
- Manuscript Received: 23 APR 2014
- Austrian Science Funds. Grant Number: P22834
- alternative splicing;
- de novo assembly;
- Drosophila simulans ;
- genome annotation;
- transcriptome reconstruction
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.