Evolution of the genomes of two nematodes in the ... - Ken Wolfe

Summary
The soil-dwelling nematode Caenorhabditis elegans has been intensively studied as a model organism for
the last 40 years. It was the first animal for which we had a complete description of development, anatomy,
a neural wiring diagram, and, in 1998, a genome sequence. In 2001 the genome of Caenorhabditis briggsae
was sequenced. They are the first pair of animals from the same genus to have their genomes sequenced.
The two worms are very similar morphologically and follow similar developmental programs, but are
surprisingly dissimilar genetically. I compared their genomes to identify syntenic regions that have been
conserved since they diverged 80–110 million years ago. I found the rate of chromosomal rearrangement to
be exceptionally high in these nematodes compared to in most eukaryotes. After the C. briggsae genome
was sequenced in 2001, an important step was the prediction of protein coding genes in the raw sequence.
I describe how my collaborators and I predicted genes in the C. briggsae genome; compared C. briggsae
genes to those of C. elegans; and used similarity to C. briggsae to improve gene predictions in C. elegans.
Intron-exon structure has evolved rapidly: I estimated there have been 0.005 intron gains or losses per
gene per million years since the two species diverged. To elucidate the mechanism of intron gain, I
pinpointed intron-exon differences that were due to intron gain rather than loss. My results narrow down
the probable mechanism of intron gain to just two of the five hypothesised mechanisms.
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