Using Nanopore Sequencing to Study the Relationship Between Mitochondrial DNA Replication/Transcription and the Non-coding Region in Caenorhabditis Species (PI: Dr. Runsheng Li)
Mitochondrial DNA (mtDNA) replication and transcription have long been a hot topic in evolutionary biology. It is well established that mtDNA is replicated through a mechanism called D-loop in nearly all species. However, recent studies have demonstrated that mtDNA in Caenorhabditis elegans is replicated by a unique mechanism called “rolling cycle”. We have recently assembled the full-length of mtDNAs for 14 Caenorhabditis species using existing NGS data. Surprisingly, we found multiple novel Non-Coding Regions (NCRs) in the mtDNAs of a subset of the 14 species which are near in position, suggesting a vital role of these NCRs in mtDNA replication or transcription. To test the hypothesis, capability of capturing full-length mtDNA and its derived RNAs would be critical for pinpointing the roles of NCRs in DNA replication and transcription. We propose to address the question using a third-generation sequencing technology called Nanopore, which produces sequencing reads of unusual length up to tens of kilo base pairs, leading to a possibility of capturing DNA or primary or mature transcripts in full length. The roles of the NCRs would emerge by comparing their positioning in the intermediates of newly replicated DNA or synthesized primary or mature transcripts. Comparative analysis of the expression of mitochondrial related genes between C. briggsae and its sister species C. nigoni and their hybrids may provide insight into the role of the NCRs in hybrid incompatibility between the two species.