The mean gene density of clusters was then compared to this distribution.
The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species.
Although gene density appears to be generally weakly (though significantly) correlated with recombination in Pearson correlations, with Chr3 L showing the strongest positive correlation with gene density (supplementary table S1, Supplementary Material online), this is supported by the results of figure 3 where this arm had the highest mean gene density.
Micro-chromosomes displayed high recombination rate, high gene density and high G+C content (mean recombination rate, 6.8552 cM/Mb; average gene density, 23.6465 genes/Mb; G+C content, 44.5064%), which distinguished from macro-chromosomes (mean recombination rate, 3.1826 cM/Mb; average gene density, 12.1210 genes/Mb; G+C content, 39.8328%) significantly.
In general, the four strains show small variations in their numbers of CDSs, mean gene lengths, and gene densities, which arise from differences in their genome sizes.
This means that gene densities are higher in prophage genomes than in prokaryotic genomes, and most genes are packed in a few operons.
While the gene density, mean exon length and average number of exons per gene are very similar in both species, in cucumber the protein length is only slightly smaller (0.9x), and mean intron length is just 1.2 times greater.
The average coding sequence size was calculated to be 837 bp and the mean number of exons per gene was 3.1; the gene density was calculated to be 8.3 genes per 100 Kbp.
The predictions for the cucumber genome are a gene density of 10 per 100 kb, mean protein length of 349 amino acids, average number of exons per gene, exon length and intron length of 4.8, 238 bp and 483 bp, respectively, and tRNA gene density of 2.9 per Mb.
In their genomic composition, the isolates were found to have the same mean i) GC content, ii) gene length, iii) operon composition and iv) gene density.
This could mean that the observed deletion frequency for gene rich regions will be less, while it will be higher for low gene density regions.
