Origins of Recently Gained Introns in Caenorhabditis

Monday, October 20, 2003 - 3:30pm - 3:50pm
Keller 3-180
Avril Coghlan (Trinity College)
Joint work with Kenneth H. Wolfe.

The genomes of the nematodes Caenorhabditis elegans and C. briggsae both contain about 100,000 introns, of which about 6000 are unique to one species or the other. To study the origins of new introns, we used a rigorous method involving phylogenetic comparisons to animal orthologs and other nematode paralogs to identify cases where an intron content difference between C. elegans and C. briggsae was almost certainly caused by intron insertion rather than deletion. We identified 57 putative recently gained introns in C. briggsae and 112 in C. elegans. Novel introns have a stronger exon splice site consensus sequence than the general population of introns, and they show the same preference for phase 0 sites in codons over phases 1 and 2 as seen in the general population. More of the novel introns are inserted in genes that are expressed in the germline than expected by chance. As compared to matched control sets of C. briggsae introns, the novel introns in C. briggsae are more likely to contain an annotated repeat element (1.7-fold; P = 0.011), and the ends of the intron are more likely to be close to the ends of the repeat element (1.5-fold; P = 0.029). Similar but weaker trends are also seen in C. elegans novel introns. One family of C briggsae repeat elements, which is related to the Helitron class of putative nonautonomous transposons, is found in significantly more novel introns than reference introns (P