Genome assembly and annotation of a Drosophila simulans strain from Madagascar

Mol Ecol Resour. 2015 Mar;15(2):372-81. doi: 10.1111/1755-0998.12297. Epub 2014 Jul 14.


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.

Keywords: Drosophila simulans; RNA-Seq; alternative splicing; de novo assembly; genome annotation; pseudogenes; transcriptome reconstruction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Drosophila / classification
  • Drosophila / genetics*
  • Genome, Insect*
  • Madagascar
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Sequence Analysis, DNA*

Associated data

  • SRA/SRX504933