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SNP markers retrieval for a non-model species: a practical approach

Arwa Shahin1*, Thomas van Gurp3, Sander A Peters2, Richard GF Visser1, Jaap M van Tuyl1 and Paul Arens1

Author Affiliations

1 Wageningen University and Research Centre, Plant Breeding, P.O. Box 16, 6700 AJ Wageningen, The Netherlands

2 Wageningen University and Research Centre, Bioscience, P.O. Box 16, 6700 AJ Wageningen, The Netherlands

3 Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, P.O. Box 50, 6700 AB Wageningen, The Netherlands

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BMC Research Notes 2012, 5:79  doi:10.1186/1756-0500-5-79

Published: 29 January 2012



SNP (Single Nucleotide Polymorphism) markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC) on 454 data from four lily genotypes and compared results with respect to SNP retrieval.


CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs.


In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.