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

David A Rasmussen,Mohamed Af Noor

doi:10.1186/1471-2164-10-382

Abstract

BackgroundThe 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.ResultsRandom pyrosequencing of the M. scalaris genome provided a depth of coverage (0.05-0.1x) 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.ConclusionWe conclude that low-coverage genome surveys are effective at generating useful information about organisms currently lacking genomic sequence data.

Highlights

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
Our preliminary sequencing of the Megaselia scalaris genome resulted in extremely low-coverage, we were able to perform a number of bioinformatic analyses that provided useful information for characterizing this genome as well as generating various genomic resources
We were able to generate genomic resources for Megaselia scalaris with very limited sequence data obtained through 454-pyrosequencing

Summary

Introduction

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. While completely assembled genomes of non-model organisms may not be obtained, very low-coverage shotgun sequencing can be used for various applications, such as to identify microsatellites for population genetic analyses [2,3]. Low coverage genome survey sequences (GSS) can provide information about gene content, polymorphisms, functional elements and repetitive elements [4]. As a case in point, the original 1.5× assembly of the dog genome provided partial sequence of thousands of dog orthologs of human genes [6]. A large fraction of the repetitive DNA sequences in the complex, highly repetitive barley genome of were (page number not for citation purposes)

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Discussion

Conclusion