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
David A Rasmussen, Mohamed A F Noor


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.


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Datasets Mentioned


Methods Mentioned

flow cytometry
454 sequencing

Related Concepts

Sequence Determinations, DNA
Tetranucleotide Repeats
Computational Molecular Biology
Interspersed Repetitive Sequences
Genome, Insect
Genome, Mitochondrial
Case-Control Studies

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