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

BMC Genomics. 2009 Aug 18;10:382. doi: 10.1186/1471-2164-10-382.

Abstract

Background: 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.

Results: 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.

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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Diptera / genetics*
  • Drosophila / genetics
  • Female
  • Genome, Insect*
  • Genome, Mitochondrial
  • Genomics / methods
  • Interspersed Repetitive Sequences
  • Male
  • Microsatellite Repeats
  • Sequence Analysis, DNA / methods*