Browsing by Author "Chandrasekaran, Sinduja"

NGS technologies and the advancement of bioinformatics methodologies have led to the start and success of many projects in genomics. One such project is the Caenorhabditis genome project, aimed at generating draft genomes for all the known and non-sequenced Caenorhabditis species. Except for C. elegans, the model organism responsible for discoveries such as the molecular mechanism of cell death and RNA interference, not much is known about other species in this genus. This hinders our understanding of the evolution of C. elegans and its distinct characteristics. This project is therefore an initiative to understand the Caenorhabditis genus. The aim of my project was to sequence and annotate the genome of Caenorhabditis doughertyi, as a part of the Caenorhabditis Genome Project. C. doughertyi is the sister species of C. brenneri, which is known for its high level of polymorphism among eukaryotes. It was initially found in the regions of Kerala, India by MA Felix in 2007 and consists of both male and female adults. The sequencing of C. doughertyi would pave the way for understanding the evolution of high diversity levels observed in C. brenneri. The raw data of the genome consisted of two paired-end libraries with insert size of 300- and 500 bp, with read lengths of 125 bp. The quality of reads was ensured by quality control measures such as trimming of adaptor sequences, error correction and removal of DNA from non-target organisms. The reads were then assembled using multiple assemblers and ABySS was decided as the best assembly based on metrics such as N50 and biological parameters like CEGMA. The draft genome was then annotated using MAKER pipeline and the orthologs were identified using OrthoMCL. The obtained draft genome can aid in preliminary comparative genomic analyses with other species in the genus. Further work may focus on improving the quality of this draft assembly towards a publication quality genome sequence for this species. ACM Computing Classification System (CCS): Life and medical sciences -> Computational biology Life and medical sciences -> Bioinformatics