3D genomic insights of an early branching metazoan : a chromosome scale assembly of Mnemiopsis leidyi and differential expression in early development
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Barclay, Charlotte
issued: 2023-08-31T23:42:08Z
issued: 2023
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: The transition to multicellularity is widely considered a crucial evolutionary process, yet the precise mechanisms are still being uncovered. Advancements in bioinformatic techniques and high-throughput DNA sequencing provide increasing opportunities to better understand complex phenomena like multicellularity, through the study of early branching model organisms. However, to fully leverage the available tools, high quality reference genomes are required. As a result an increasing number of studies combine long read and HiC sequence data to generate a high quality, chromosome scale assembly with high contiguity. This study utilises PacBio's novel long and accurate HiFi reads, in conjunction with Hi-C sequencing technology, to produce a chromosome-scale assembly for the ctenophore Mnemiopsis leidyi. The final assembly demonstrates remarkable contiguity, with an N50 value of 15.6MB and a computationally derived karyotype of n=13. These findings demonstrate an improvement of greater than two orders of magnitude when compared to the previous short read assembly for this species. Further structural genomic organisation was identified, using Arrowhead as part of the Juicer pipeline, to provide the first evidence of topologically associating domains (TADs) and loops in this organism. These findings highlight the importance of utilizing advanced sequencing technologies to improve existing assemblies in our understanding of genomic organisation and structure, and the considerations that should be taken when comparing results derived from different bioinformatic tools. Mnemiopsis leidyi is phylogenetically well placed to answer evolutionary questions surrounding the origins of multicellularity and the addition of a high-quality reference assembly will prove imperative to future molecular and genomics research.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/85762
note: 3D GENOMIC INSIGHTS OF AN EARLY BRANCHING METAZOAN: A CHROMOSOME SCALE ASSEMBLY OF MNEMIOPSIS LEIDYI AND DIFFERENTIAL EXPRESSION IN EARLY DEVELOPMENT by Charlotte Barclay MSci (Hons), The University of Southampton, 2013 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2023 © Charlotte Barclay, 2023 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the thesis entitled: 3D genomic insights of an early branching metazoan: a chromosome scale assembly of Mnemiopsis leidyi and differential expression in early development submitted by Charlotte Barclay in partial fulfilment of the requirements for the degree of Master of Science in Bioinformatics Examining Committee: Dr Steven Plotkin, Professor, Physics and Astronomy, UBC Supervisor Dr Wyeth Wasserman, Professor, Medical Genetics, UBC Supervisory Committee Member Dr Sheila Teves, Assistant Professor, Biochemistry, UBC Supervisory Committee Member iii Abstract The transition to multicellularity is widely considered a crucial evolutionary process, yet the precise mechanisms are still being uncovered. Advancements in bioinformatic techniques and high-throughput DNA sequencing provide increasing opportunities to better understand complex phenomena like multicellularity, through the study of early branching model organisms. However, to fully leverage the available tools, high quality reference genomes are required. As a result an increasing number of studies combine long read and HiC sequence data to generate a high quality, chromosome scale assembly with high contiguity. This study utilises PacBio's novel long and accurate HiFi reads, in conjunction with Hi-C sequencing technology, to produce a chromosome-scale assembly for the ctenophore Mnemiopsis leidyi. The final a…
has type: Thesis/Dissertation
date issued: 2023-11
is shown at: 10.14288/1.0435712
language: eng
degree discipline: Bioinformatics
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
contributor: Plotkin, Steven
type: Text
identifier URI: http://hdl.handle.net/2429/85762