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

Chapter 3
The Caenorhabditis briggsae Gene
Set
During 2001 the Washington University Genome Sequencing Center and the Sanger Institute sequenced
the Caenorhabditis briggsae genome, producing a high quality draft that covers 98% of the ∼104-Mb
genome. I was fortunate to collaborate on the C. briggsae Sequencing Project during my Ph.D.. This chap-
ter consists of sections I wrote for the C. briggsae genome paper describing my work on the project (Stein
et al., 2003; to be published in the November 2003 issue of PLoS Biology).
ABSTRACT
We predict about 19,500 protein coding genes in the C. briggsae genome, roughly the same number of genes
as in C. elegans. Of the C. briggsae genes, 12,100 have clear C. elegans orthologues, a further 6500 have
one or more clearly detectable C. elegans homologues, and about 800 genes have no detectable matches
in C. elegans. Among the introns in orthologue pairs, 6579 (9%) are species-specific introns, two-thirds of
which are C. elegans-specific. The C. briggsae draft sequence will greatly improve the annotation of the
C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1300 new C. elegans
genes.
3.1 INTRODUCTION
The compactness of the 100-Mb C. elegans genome facilitates ab initio gene prediction methods, but even
the best of these fails to find some genes, and boundaries of genes and exons remain problematic (Reboul
et al., 2003). As many as 50% of C. elegans gene predictions contain major or minor errors (Reboul
et al., 2003). One motivating factor for sequencing the entire C. briggsae genome was the promise that
comparison between the two genomes would help to correct C. elegans predicted gene structures. We
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