Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina-tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution.
FANG LinYE JiaLI NingZHANG YongLI SongGangGANE Ka-Shu WONGWANG Jun
Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold.Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants.Our protocol is also well suited for use with whole genome amplified DNA.The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.
