Figure 6

Whole-chromosome view of (a) transcriptome map (plotting running medians of gene expression values along chromosome 1 with window size of 39 genes); (b) transcriptome map on separate strands (plotting running medians of gene expression values on separate strands with window size of 19 genes on each individual strand (left side: + strand; right side: - strand) along chromosome 1); (c) gene density (gene density was defined as number of genes per 100 kb genomic region, running medians of gene densities with window size 39 gene were plotted along chromosome 1); (d) GC content; (e) gene length; (f) average intron length (GC content, gene length, and average intron length were calculated for each gene, the running medians of values for those three features with a window size of 39 genes were plotted along chromosome 1); (g) "minimal intron" density (the minimal intron here were defined as introns sizing from 50 to 150 bp, and minimal intron density was defined as the number of minimal introns per 500 kb genomic region, then the running medians of minimal intron intensities with window size of 39 genes were ploted along chromosome 1); and (h) recombination rate (recombination rate data of chicken chromosome 1 was obtained from previous study by Groenen et al.[25], and plotted in the same way as described by Groenen et al.) plotted on chicken chromosome one. The start of the chromosome corresponds with the top of the plot.