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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in
Nathalie J van Orsouw1, René C J Hogers, Antoine Janssen
1Keygene NV, Wageningen, The Netherlands. nathalie.van-orsouw@keygene.com
Plos One
|November 15, 2007
Summary
We developed CRoPS, a novel method for discovering single nucleotide polymorphisms (SNPs) in low polymorphic species. This cost-effective approach combines genome complexity reduction with next-generation sequencing, making SNP discovery affordable.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Single nucleotide polymorphisms (SNPs) are crucial for biomedical research but challenging to discover in species with low polymorphism.
- Existing Sanger sequencing technology is insufficient for cost-effective SNP discovery in such species.
- High levels of repetitive DNA and low polymorphism in germplasm further complicate SNP identification.
Purpose of the Study:
- To introduce CRoPS (Complexity Reduction of Polymeric Sequences) as a novel, cost-effective method for SNP discovery.
- To leverage reproducible genome complexity reduction (AFLP) with next-generation sequencing (GS FLX) for efficient polymorphism identification.
- To enable affordable SNP discovery in organisms with complex genomes and limited genetic variation.
Main Methods:
- CRoPS combines Amplified Fragment Length Polymorphism (AFLP) for genome complexity reduction with Genome Sequencer (GS) FLX next-generation sequencing.
- Hundreds of thousands of sequence reads from complexity-reduced genomes of multiple samples are processed.
- A fully-automated bioinformatics pipeline is employed to mine for SNPs.
Main Results:
- CRoPS successfully identified numerous putative SNPs in maize.
- Over 75% of discovered SNPs were validated using SNPWave assays, confirming their accuracy.
- Validated SNPs originated from unique, single-copy genome sequences.
Conclusions:
- CRoPS offers an affordable solution for SNP discovery in organisms with high repetitive DNA content and low polymorphism.
- The method eliminates the need for prior sequence information, broadening its applicability.
- CRoPS revolutionizes polymorphism discovery for genetic research and breeding programs.
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