Skip to main content

Homology and evidence-based genome annotation of Caenorhabditis species

Resource type
Thesis type
(Thesis) M.Sc.
Date created
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.
Copyright statement
Copyright is held by the author.
The author granted permission for the file to be printed and for the text to be copied and pasted.
Scholarly level
Supervisor or Senior Supervisor
Thesis advisor: Chen, Jack
Download file Size
etd6371_BUyar.pdf 1.75 MB

Views & downloads - as of June 2023

Views: 0
Downloads: 1