Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput...

Area of Science:

• Genomics
• Bioinformatics
• Population Genetics

Background:

• Second-generation sequencing enables large-scale DNA variation studies.
• Developing methods for high-throughput SNP discovery is crucial for species lacking sequenced reference genomes.
• This study focuses on Meleagris gallopavo (turkey) due to its importance and lack of a reference genome.

Purpose of the Study:

• To establish an efficient and cost-effective pipeline for de novo SNP discovery.
• To identify a substantial number of high-quality SNPs in the turkey genome.
• To demonstrate the utility of the pipeline in a non-model organism.

Main Methods:

• Utilized a short-read de novo assembler and a variation-calling program.
• Generated 100 million 36 bp reads from a 2-3 kbp genome fraction of pooled turkey individuals.
• Assembled reads into contigs and identified SNPs with high reliability (>90%).

Main Results:

• Identified over 7,500 SNPs initially, increasing to over 11,000 with additional public data.
• Achieved a 95% SNP conversion rate in genotyping a subset of 340 SNPs.
• Demonstrated uniform distribution of assembled contigs across the turkey genome.

Conclusions:

• The developed pipeline is efficient and cost-effective for SNP identification in genomes lacking sequencing.
• The methodology successfully identified thousands of high-quality SNPs in turkey.
• The approach ensures an even distribution of identified SNPs across the targeted genome.