Author: Uyar, Bora
I have re-annotated the genomes of four sister species of the model organism Caenorhabditis elegans: C. briggsae, C. remanei, C. brenneri, and C. japonica, using a homology-based gene predictor genBlastG. Compared to the existing gene sets of these four species, genes of the revised gene sets demonstrate higher conservation with their orthologs in C. elegans as well as more ortholog pairs. I have validated and further revised the C. briggsae gene set, through next-generation short read sequencing of the transcriptome. In the revised C. briggsae gene set (23,159 genes), 7,347 genes (33.9% of all genes with introns) have all introns confirmed. Of all introns in the revised gene set (103,083), 62,727 (60.9%) are confirmed. Additionally, I have identified 1,034 operons in C. briggsae, with 532 (51.4%) perfectly conserved in C. elegans. This study sets up a solid platform for comparative genomics analysis and evolutionary studies of Caenorhabditis species.
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Thesis advisor: Chen, Jack
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