Employing Limited Next Generation Sequence Data for the Development of Genetic Loci of Phylogenetic and Population Genetic Utility

Publication Year:
2015
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Repository URL:
http://digitalcommons.fiu.edu/etd/2191
DOI:
10.25148/etd.fidc000108
Author(s):
Evenstone, Lauren
Publisher(s):
Florida International University
Tags:
Genetic; PCR; Chrysomya; Mitochondrial genome; Next Generation Sequencing; NGS; CLC; genomics; Blowfly; Bioinformatics; Computational Biology; Entomology; Genetics; Genomics; Molecular Genetics
thesis / dissertation description
Massively parallel high throughput sequencers are transforming the scientific research by reducing the cost and time necessary to sequence entire genomes. The goal of this project is to produce preliminary genome assemblies of calliphorid flies using Life Technologies’ Ion Torrent sequencing and Illumina’s MiSeq sequencing. I located, assembled, and annotated a novel mitochondrial genome for one such fly, the little studied Chrysomya pacifica that is central to one hypothesis about blow fly evolution. With sequencing data from Chrysomya megacephala, its forensically relevant sister species, much insight can be gained by alignments, sequence and protein analysis, and many more tools within the CLC Genomics Workbench software program. I present these analyses here of these recently diverged species.