What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae).

Journal Article (Journal Article)


The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, completely assembled genome sequences for most non-model organisms remains challenging, low-coverage genome survey sequences (GSS) can provide a wealth of biologically useful information at low cost. Here, using a random pyrosequencing approach, we sequence the genome of the scuttle fly Megaselia scalaris and evaluate the utility of our low-coverage GSS approach.


Random pyrosequencing of the M. scalaris genome provided a depth of coverage (0.05x0.1x) much lower than typical GSS studies. We demonstrate that, even with extremely low-coverage sequencing, bioinformatics approaches can yield extensive information about functional and repetitive elements. We also use our GSS data to develop genomic resources such as a nearly complete mitochondrial genome sequence and microsatellite markers for M. scalaris.


We conclude that low-coverage genome surveys are effective at generating useful information about organisms currently lacking genomic sequence data.

Full Text

Duke Authors

Cited Authors

  • Rasmussen, DA; Noor, MAF

Published Date

  • August 2009

Published In

Volume / Issue

  • 10 /

Start / End Page

  • 382 -

PubMed ID

  • 19689807

Pubmed Central ID

  • PMC2735751

Electronic International Standard Serial Number (EISSN)

  • 1471-2164

International Standard Serial Number (ISSN)

  • 1471-2164

Digital Object Identifier (DOI)

  • 10.1186/1471-2164-10-382


  • eng