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Megaselia scalaris genome

ABSTRACT: Megaselia scalaris genome assembly

PROVIDER: PRJEB1273 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	CAQQ02.dat.gz	Other
	CAQQ02.fasta.gz	Fasta.gz
	CAQQ02.master.dat	Other
	CAQQ01.dat.gz	Other

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Megaselia scalaris

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

Project description: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.

| S-EPMC2735751 | biostudies-literature

How big is your Y? A genome sequence-based estimate of the size of the male-specific region in Megaselia scalaris.

Project description:The scuttle fly, Megaselia scalaris, is often cited as a model in which to study early sex chromosome evolution because of its homomorphic sex chromosomes, low but measurable molecular differentiation between sex chromosomes, and occasional transposition of the male-determining element to different chromosomes in laboratory cultures. Counterintuitively, natural isolates consistently show sex linkage to the second chromosome. Frequent natural transposition of the male-determining element should lead to the loss of male specificity of any nontransposed material on the previous sex-linked chromosome pair. Using next-generation sequencing data from a newly obtained natural isolate of M. scalaris, we show that even highly conservative estimates for the size of the male-specific genome are likely too large to be contained within a transposable element. This result strongly suggests that transposition of the male-determining region either is extremely rare or has not persisted recently in natural populations, allowing for differentiation of the sex chromosomes of this species.

| S-EPMC4291468 | biostudies-literature

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