Project Title
Whole Genome Sequencing for the Millipede Cherokia georgiana
Faculty Mentor(s) Name(s)
Dr. Bruce Snyder and Dr. Arnab Sengupta
Abstract
Despite the incredible diversity seen in thousands of millipede species, only five genomes have ever been fully sequenced. Limited genetic information is currently available on these crucial decomposers, particularly in understanding cyanogenic gene expression under stressed conditions. The focus of our research pertains to one common Appalachian millipede species known to produce the defensive chemical hydrogen cyanide. Our current research goal is to de novo sequence the genome of the millipede Cherokia georgiana in its entirety, which will enable further research into gene expression. While the genes involved in cyanide secretion have been identified, this biochemical pathway found in the Polydesmida is poorly understood. The entire genomic sequence will also advance the current understanding of this species’ phylogenetic importance to other North American species. First, DNA will be extracted using kits designed to extract high molecular weight (HMW) DNA used for next-generation sequencing (NGS). NGS library quality will be evaluated using the Agilent TapeStation 4200 automated electrophoresis system. NGS will be carried out using a combination of long-read (Oxford Nanopore MinION, PacBIO) and short-read (Illumina) sequencing platforms. The assembled genome will be compared to existing millipede genomic data, and sequences conserved across eukaryotic genomes. This will facilitate further research in using RNA-seq analysis to elucidate actively transcribed genes under stressed conditions.
Whole Genome Sequencing for the Millipede Cherokia georgiana
Despite the incredible diversity seen in thousands of millipede species, only five genomes have ever been fully sequenced. Limited genetic information is currently available on these crucial decomposers, particularly in understanding cyanogenic gene expression under stressed conditions. The focus of our research pertains to one common Appalachian millipede species known to produce the defensive chemical hydrogen cyanide. Our current research goal is to de novo sequence the genome of the millipede Cherokia georgiana in its entirety, which will enable further research into gene expression. While the genes involved in cyanide secretion have been identified, this biochemical pathway found in the Polydesmida is poorly understood. The entire genomic sequence will also advance the current understanding of this species’ phylogenetic importance to other North American species. First, DNA will be extracted using kits designed to extract high molecular weight (HMW) DNA used for next-generation sequencing (NGS). NGS library quality will be evaluated using the Agilent TapeStation 4200 automated electrophoresis system. NGS will be carried out using a combination of long-read (Oxford Nanopore MinION, PacBIO) and short-read (Illumina) sequencing platforms. The assembled genome will be compared to existing millipede genomic data, and sequences conserved across eukaryotic genomes. This will facilitate further research in using RNA-seq analysis to elucidate actively transcribed genes under stressed conditions.