HCNSO Student Theses and Dissertations

Defense Date

12-6-2017

Document Type

Thesis

Degree Name

M.S. Marine Biology

First Advisor

Jose Lopez

Second Advisor

Charles Messing

Third Advisor

Stephen Grant

Abstract

Genomic analysis provides a substantial amount of information on evolutionary history, novel genes, transcriptomic expression and regulation in response to environmental stimuli, how efficiently organisms utilize their genome, and directional genome evolution. Genome size analysis serves as the first step in the sequencing process, because sequencing and annotation costs are directly correlated with genome size. Invertebrates represent the vast majority of faunal diversity on the planet, and, to a greater extent, the marine environment, although they are vastly understudied when compared to vertebrate genomes. Flow cytometry is a widely used, reliable, and accurate means of estimating genome sizes and has yielded valid measurements in this comparatively broad taxonomic study. This methodology quantifies genome sizes by measuring the fluorescent re-emission from nuclei that have been saturated with DNA- intercalating dyes, such as propidium iodide. Genome sizes of 19 species across five phyla were estimated by comparison with the known genome size of chicken (Gallus domesticus). Several estimates reported here are the first for their species or class. In addition to estimating new marine invertebrate genome sizes, analyses of some common preservation methods of tissue viability for flow cytometric estimations were performed. Generally, in comparison to RNAlater or ethanol, DMSO-based storage buffer was most successful at preserving nuclear membrane integrity, a requirement for flow cytometric genome size estimations. Recommendations of cost-effective species eligible for current next-generation sequencing technology (<3.5 Gb) are given for invertebrate genomicists seeking potential novel species to sequence.

ORCID ID

0000-0003-1595-8142

Researcher ID

A-5298-2018

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