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ERX012705: Multiplexed Microsatellite Recovery Using Massively Parallel Sequencing
1 ILLUMINA (Illumina Genome Analyzer II) run: 412,682 spots, 62.7M bases, 43.5Mb downloads

Design: Microsatellite Recovery from multiplexed and barcoded samples-- two species of conifers and five species of birds-- using massively parallel sequencing
Submitted by: USDA-FS
Study: Multiplexed Microsatellite Recovery Using Massively Parallel Sequencing
show Abstracthide Abstract
Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method due to the comparatively low cost of marker development, ease of analysis, and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite enriched, barcoded genomic libraries from diverse taxa (two conifers trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80 bp reads. In this experiment, we recovered 6.1 million sequences, 1.4 million of which contained dinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favorably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering sequence capacity of modern sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $500 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as .threatened. and .endangered. in the United States for under $0.7M.
Sample: Coturnicops noveboracensis
SAMEA758623 • ERS032623 • All experiments • All runs
Library:
Name: S3
Instrument: Illumina Genome Analyzer II
Strategy: WCS
Source: GENOMIC
Selection: PCR
Layout: PAIRED
Construction protocol: Illumina Paired End library construction protocol, Part #1003880 Rev. A, with adapters modified as previously reported (Cronn et al., 2008, Nucleic Acids Research)
Spot descriptor:
forward77  reverse

Runs: 1 run, 412,682 spots, 62.7M bases, 43.5Mb
Run# of Spots# of BasesSizePublished
ERR034179412,68262.7M43.5Mb2011-04-26

ID:
68441

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