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.

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

Figure 1

Map of the M. scalaris Mitochondrial Genome. Map of the M. scalaris mitochondrial genome showing the positions of the protein-coding genes (green arrows), 16S ribosomal RNAs (red line) and the gaps in our sequence (external yellow arrows).

Figure 2

Sequence Coverage Across the M. scalaris Mitochondrial Genome. The depths of coverage, averaged across 25 bp windows, attained from genome survey sequences of the mitochondrial genome of M. scalaris. The vertical axis represents the number of nucleotide bases with the corresponding depth of coverage.