Megaselia scalaris (Msca1)

Megaselia scalaris Assembly and Gene Annotation

About Megaselia scalaris

Megaselia scalaris is a scuttle fly of the Phoridae family, also known as the coffin fly or humpbacked fly [1]. Originally from warm climates, the species is synanthropic and is now found near human habitations worldwide. These tiny flies are omnivorous in the broadest sense of the term, eating almost anything, dead or alive, from bacteria to mammals; and even manage to survive on just blue paint or boot polish [2]. The name 'coffin fly' derives from their ability to get through tiny cracks in coffins in order to feed on the corpse, and forensic evidence based on the presence of M. scalaris can be used to infer a postmortem interval (if sufficient precautions are taken - see discussion in [2]).

Phylogenetically, M. scalaris lies between mosquitoes and fruitflies [3], and thus may be useful in dipteran comparative studies. This species also has potential as a model organism because it is amenable to manipulation in a laboratory, and has different neurological and physiological properties to Drosophila melanogaster; it may be particularly suited to studying mechanisms of sex determination [4].

Picture credit (Creative Commons BY 3.0): Charles Schurch Lewallen 2005


The Durham, NC isolate 2 strain of Megaselia scalaris was sequenced by the Noor lab at Duke, generating ~303Mb with contig N50=932. Contigs were assembled into 231,743 scaffolds, 702 of which derive from pairwise alignments with Drosophila melanogaster or Glossina morsitans.


Genes were predicted for Megaselia scalaris using the MAKER pipeline, resulting in 11,461 protein-coding genes. Non-coding RNA genes were added using the Ensembl Genomes pipeline, and BLAST hits and protein features have been computed.


  1. The scuttle fly.
    Varney RL, Noor MA. 2010. Current Biology. 20:R466-7.
  2. Natural history of the scuttle fly, Megaselia scalaris.
    Disney RH. 2008. Annual Review of Entomology. 53:39-60.
  3. Episodic radiations in the fly tree of life.
    Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim JW, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM et al. 2011. PNAS. 108:5690-5695.
  4. New Y chromosomes and early stages of sex chromosome differentiation: sex determination in Megaselia.
    Traut W. 2010. Journal of Genetics. 89:307-313.

More information

General information about this species can be found in Wikipedia.



AssemblyMsca1, INSDC Assembly GCA_000341915.1, Feb 2013
Database version107.1
Golden Path Length490,071,573
Genebuild byEnsembl Metazoa
Genebuild methodFull genebuild
Data sourceEnsembl Metazoa

Gene counts

Coding genes11,461
Non coding genes236
Small non coding genes234
Long non coding genes2
Gene transcripts11,699