Analysis of changes in recombination landscape from S. paradoxus in different environments
Meiotic recombination occurs at different frequencies across positions within eukaryote genomes, generating a recombination landscape with hot and cold spots. Previous studies use sequencing of individual progeny or ChIPseq of DSBs, among other techniques, to analyse recombination landscapes. Recombination hotspots are associated with several epigenetic markers, including histone H3K4 methylations deposited by RNA polymerase. Little has been done to explore the effect of environment on recombination landscapes. Here, we  studied how environmental effects on transcription affect the recombination landscape of heterozygote diploid Saccharomyces paradoxus in different environments. Genetically identical populations were grown in media containing either glucose or galactose as a carbon source, or grown at 30?C or 25?C on glucose before inducing meiosis. Differential transcription was confirmed using RNA sequencing. Haploid meiotic progeny were genetically sequenced at 1,000x depth, and reads were individually categorized as recombinant or parental based on variant positions, and normalized by sequencing depth. Using this measure, we generated recombination landscapes in different environments. Genome-wide recombination landscapes at a resolution of 10Kb presented stronger correlations between samples within treatments than would be expected with random effects. Changes in local recombination rates may alter the degree of linkage between contiguous genes, modifying the genetic composition of the progeny.