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.
%0 Journal Article
%1 rasmussen2009genome
%A Rasmussen, D A
%A Noor, M A
%D 2009
%J BMC Genomics
%K Megaselia low_coverage phorids
%P 382-382
%R 10.1186/1471-2164-10-382
%T What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae)
%U http://www.ncbi.nlm.nih.gov/pubmed/19689807?dopt=Abstract&holding=f1000,f1000m,isrctn
%V 10
%X 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.
@article{rasmussen2009genome,
abstract = {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.},
added-at = {2013-01-15T23:31:21.000+0100},
author = {Rasmussen, D A and Noor, M A},
biburl = {https://www.bibsonomy.org/bibtex/2e219d9f432bc5b2b76aed7fd814e4872/peter.ralph},
doi = {10.1186/1471-2164-10-382},
interhash = {a1c6852c919c0e2c72c740abcca303bc},
intrahash = {e219d9f432bc5b2b76aed7fd814e4872},
journal = {BMC Genomics},
keywords = {Megaselia low_coverage phorids},
pages = {382-382},
pmid = {19689807},
timestamp = {2013-01-15T23:31:21.000+0100},
title = {What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly {\it Megaselia scalaris} (Phoridae)},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19689807?dopt=Abstract&holding=f1000,f1000m,isrctn},
volume = 10,
year = 2009
}