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The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics

Figure 6

Evolutionary Divergence across C. elegans Chromosome V

Each panel corresponds to a C. elegans chromosome, and the individual tracks show different measurements of evolutionary divergence.

(A) Regions of synteny (colinearity) between C. elegans and C. briggsae. White areas correspond to areas where the two genomes could not be aligned owing to divergence and are more abundant in the chromosome arms.

(B) C. elegans gene density and genetic map position. Gene density is plotted as a histogram, showing a relatively uniform distribution of genes across each chromosome. The relationship of the position of genes on the genetic map to their position on the sequence is superimposed on the y-axis. Steeper slopes in this plot indicate higher rates of meiotic recombination. Inflection points in the genetic map plot reflect the division of the chromosomes into recombinationally active “arms” and recombinationally slow “centers.”

(C) C. briggsae/C. elegans orthologs normalized for gene density in 100 kbp sliding windows. Prominent regions of low ortholog density are seen on chromosome arms.

(D) C. elegans “orphans,” genes with no significant protein similarity in C. briggsae or the non-C. elegans portion of SwissProt. This histogram has been normalized for gene density in 100 kbp sliding windows. Spikes in orphan density seem to correlate with regions of low ortholog density.

(E) C. elegans genes that mutate to lethality or are lethal in RNAi screens, in 100 kbp sliding windows normalized to overall gene density. This track shows the distribution of essential genes and demonstrates their tendency to cluster in the chromosome centers.

(F) Repetitive elements, binned in 100 kbp sliding windows. Repeat-rich regions correlate with both the absence of significant syntenic coverage and ortholog-poor regions.

(G) The KA/KS ratio in ortholog pairs. Lower values indicate greater levels of purifying selection.

(H) The rate of KS within ortholog pairs, in 100 kbp sliding windows.

Figure 6

doi: https://doi.org/10.1371/journal.pbio.0000045.g006