Whole genome sequencing century-old ethanol-preserved Philippine fishes

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dc.contributor.advisorBird, Christopher
dc.contributor.authorRoberts, Roy Lonnie
dc.contributor.committeeMemberSeemann, Frauke
dc.contributor.committeeMemberPortnoy, David
dc.creator.orcidhttps://orcid.org/0000-0002-9056-7208
dc.date.accessioned2024-01-05T22:48:33Z
dc.date.available2024-01-05T22:48:33Z
dc.date.issued2023-08
dc.descriptionA thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Fisheries and Maricultureen_US
dc.description.abstractThe genomes of organisms stored in museums hold a wealth of information that is challenging to access. Recent success in sequencing desiccated museum insects involved using Whole Genome Amplification (WGA) and enzymatic repair of deoxyribose nucleic acid (DNA) damage. However, these techniques have not been tested on fishes preserved in ethanol for over a century. Here, I tested for the effects of WGA, repair, and the amount of template DNA on whole genome sequencing of historical (1908-09) and contemporary (2017-19) Philippine reef fishes. I attempted to construct 178 shotgun libraries (Illumina 2 x 150bp, 92 contemporary, 86 historical) using commercial kits and successfully produced 130 libraries (86 contemporary, 44 historical). Contrary to expectation, WGA had a negative effect on success of libraries, and repair had a small number of minor positive effects. A greater proportion of historical libraries treated with WGA failed than those that were not (37% +WGA, 65% -WGA, p=0.007). While the -WGA, historical libraries that succeeded produced less reads per unit effort than contemporary libraries (p=1.60E-07), this can be addressed by increasing the amount of DNA from historical specimens in the sequencing library. Increasing the template DNA mass was one of the best ways to improve library success, except when WGA was employed. However, only a limited amount of DNA can be obtained from historical samples using a standard commercial kit, and it would be useful to explore alternative protocols. Overall, I found the basic library preparation protocol without WGA or repair to be the best alternative for sequencing historical ethanol-preserved fish. This methodology is relatively cost-effective and can unlock the genomes of historical, ethanol-preserved fishes stored on the shelves of museums.en_US
dc.description.collegeCollege of Scienceen_US
dc.description.departmentFisheries and Maricultureen_US
dc.format.extent69 pagesen_US
dc.identifier.urihttps://hdl.handle.net/1969.6/97716
dc.language.isoen_USen_US
dc.rightsThis material is made available for use in research, teaching, and private study, pursuant to U.S. Copyright law. The user assumes full responsibility for any use of the materials, including but not limited to, infringement of copyright and publication rights of reproduced materials. Any materials used should be fully credited with its source. All rights are reserved and retained regardless of current or future development or laws that may apply to fair use standards. Permission for publication of this material, in part or in full, must be secured with the author and/or publisher., This material is made available for use in research, teaching, and private study, pursuant to U.S. Copyright law. The user assumes full responsibility for any use of the materials, including but not limited to, infringement of copyright and publication rights of reproduced materials. Any materials used should be fully credited with its source. All rights are reserved and retained regardless of current or future development or laws that may apply to fair use standards. Permission for publication of this material, in part or in full, must be secured with the author and/or publisher.en_US
dc.subjectbioinformatic processingen_US
dc.subjectmuseomicsen_US
dc.subjectnext generation sequencingen_US
dc.subjectreef habitat conservationen_US
dc.titleWhole genome sequencing century-old ethanol-preserved Philippine fishesen_US
dc.typeTexten_US
dc.type.genreThesisen_US
thesis.degree.disciplineFisheries and Mariculture
thesis.degree.grantorTexas A & M University--Corpus Christien_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US

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