Research article

Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

Ji Qi^1,3 , Asela J Wijeratne^2,3,4,7 , Lynn P Tomsho^1,3 , Yi Hu^2,3 , Stephan C Schuster^1,3 and Hong Ma^2,3,4,5,6

¹  Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA

²  Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA

³  The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA

⁴  The Intercollege Graduate Program in Plant Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA

⁵  State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, PR China

⁶  Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China

⁷  Department of Plant Cellular and Molecular Biology, the Ohio State University, Columbus OH 43210, USA

author email corresponding author email

BMC Genomics 2009, 10:475doi:10.1186/1471-2164-10-475

Published:	15 October 2009

Abstract

Background

Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loops form either crossovers (COs) or non-crossovers (NCOs), which occur at many sites in the genome. Differences at the nucleotide level associated with COs and NCOs enable us to detect these recombination events and their distributions.

Results

We used high throughput sequencing to uncover over 46 thousand single nucleotide polymorphisms (SNPs) between two budding yeast strains and investigated meiotic recombinational events. We provided a detailed analysis of CO and NCO events, including number, size range, and distribution on chromosomes. We have detected 91 COs, very close to the average number from previous genetic studies, as well as 21 NCO events and mapped the positions of these events with high resolution. We have obtained DNA sequence-level evidence for a wide range of sizes of chromosomal regions involved in CO and NCO events. We show that a large fraction of the COs are accompanied by gene conversion (GC), indicating that meiotic recombination changes allelic frequencies, in addition to redistributing existing genetic variations.

Conclusion

This work is the first reported study of meiotic recombination using high throughput sequencing technologies. Our results show that high-throughput sequencing is a sensitive method to uncover at single-base resolution details of CO and NCO events, including some complex patterns, providing new clues about the mechanism of this fundamental process.