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SNP discovery using paired-end RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)

(2013) MOLECULAR ECOLOGY RESOURCES. 13(2). p.269-275
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Single nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost-effective approaches to uncover genome-wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD-PE (Restriction site Associated DNA Paired-End sequencing) approach. RAD tags were generated from the PstI-digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired-end sequenced using Illumina technology to produce similar to 24.5Mb of sequences, covering similar to 7% of the specie's genome. Sequences were assembled into similar to 76000 contigs with a mean length of 323bp (N50=357bp, sequencing depth=24x). In all, >15000 SNPs were called, of which 47% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD-PE as an inexpensive genome-wide SNP discovery technique (success rate: 87%). In addition to SNPs, we discovered >600 putative SSR markers.
Keywords
pooling, population genomics, Pyrenean rocket, RAD paired-end sequencing, SNP discovery, SSR discovery, NEXT-GENERATION, MARKER DESIGN, POPULATIONS, MICROSATELLITES, IDENTIFICATION, EVOLUTION

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Citation

Please use this url to cite or link to this publication:

Chicago
Vandepitte, K, O Honnay, J Mergeay, P Breyne, Isabel Roldàn-Ruiz, and Tim De Meyer. 2013. “SNP Discovery Using Paired-end RAD-tag Sequencing on Pooled Genomic DNA of Sisymbrium Austriacum (Brassicaceae).” Molecular Ecology Resources 13 (2): 269–275.
APA
Vandepitte, K, Honnay, O., Mergeay, J., Breyne, P., Roldàn-Ruiz, I., & De Meyer, T. (2013). SNP discovery using paired-end RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae). MOLECULAR ECOLOGY RESOURCES, 13(2), 269–275.
Vancouver
1.
Vandepitte K, Honnay O, Mergeay J, Breyne P, Roldàn-Ruiz I, De Meyer T. SNP discovery using paired-end RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae). MOLECULAR ECOLOGY RESOURCES. 2013;13(2):269–75.
MLA
Vandepitte, K, O Honnay, J Mergeay, et al. “SNP Discovery Using Paired-end RAD-tag Sequencing on Pooled Genomic DNA of Sisymbrium Austriacum (Brassicaceae).” MOLECULAR ECOLOGY RESOURCES 13.2 (2013): 269–275. Print.
@article{3099107,
  abstract     = {Single nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost-effective approaches to uncover genome-wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD-PE (Restriction site Associated DNA Paired-End sequencing) approach. RAD tags were generated from the PstI-digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired-end sequenced using Illumina technology to produce similar to 24.5Mb of sequences, covering similar to 7\% of the specie's genome. Sequences were assembled into similar to 76000 contigs with a mean length of 323bp (N50=357bp, sequencing depth=24x). In all, {\textrangle}15000 SNPs were called, of which 47\% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD-PE as an inexpensive genome-wide SNP discovery technique (success rate: 87\%). In addition to SNPs, we discovered {\textrangle}600 putative SSR markers.},
  author       = {Vandepitte, K and Honnay, O and Mergeay, J and Breyne, P and Rold{\`a}n-Ruiz, Isabel and De Meyer, Tim},
  issn         = {1755-098X},
  journal      = {MOLECULAR ECOLOGY RESOURCES},
  keyword      = {pooling,population genomics,Pyrenean rocket,RAD paired-end sequencing,SNP discovery,SSR discovery,NEXT-GENERATION,MARKER DESIGN,POPULATIONS,MICROSATELLITES,IDENTIFICATION,EVOLUTION},
  language     = {eng},
  number       = {2},
  pages        = {269--275},
  title        = {SNP discovery using paired-end RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)},
  url          = {http://dx.doi.org/10.1111/1755-0998.12039},
  volume       = {13},
  year         = {2013},
}

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