C. briggsae genome annotation and comparative analysis with C. elegans using RNA-Seq data

Complete genome annotations are essential for comparative genomics. Currently, the C. briggsae genome annotation is incomplete that limits its utility as a comparative platform for C. elegans. Using RNA-Seq data, we have generated a more complete C. briggsae genome annotation. We identified 20,660 novel introns, 35,635 novel exons, and 5,654 novel protein-coding transcripts, and generated improved databases consisting of 123,974 introns, 150,690 exons, and 28,129 protein-coding transcripts, respectively. The improved C. briggsae annotation together with comparative analyses revealed 132 novel ortholog relationships (between C. briggsae and C. elegans) and 2 novel C. elegans protein-coding genes. This has shown that despite limited data available for C. briggsae, the improved annotation has enhanced the utility of C. briggsae as a comparative platform for C. elegans. As more RNA-Seq data becomes available, this method can be used to further refine not only C. briggsae annotation but also C. elegans annotation.