title: What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae).
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.
  
  
  CONCLUSIONS
  We conclude that low-coverage genome surveys are effective at generating useful information about organisms currently lacking genomic sequence data.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA. dar24@duke.edu
authors.forename: David A
authors.initials: DA
authors.lastname: Rasmussen
authors.forename: Mohamed A F
authors.initials: MA
authors.lastname: Noor
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004175:Diptera / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D005260:Female; D049750:Genome, Insect; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods; D020071:Interspersed Repetitive Sequences; D008297:Male; D018895:Microsatellite Repeats; D017422:Sequence Analysis, DNA / Q000379:methods*
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