The genome of black spruce : genome annotation & analyses
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Lo, Theodora
issued: 2024-01-03T23:07:37Z
issued: 2023
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: Abiotic and biotic stresses associated with climate change have been identified as a dominant cause of forest tree mortality in boreal forests. Some tree populations may have the capacity for rapid adaptation or migration to keep pace with changing environmental conditions. One species of interest is black spruce (Picea mariana [Mill.] B.S.P.) as adaptive variation in relation to climate change has previously been reported for this transcontinental North American conifer. As exhibited in studies of other economically important forest trees, genomic resources play a critical role in advancing our understanding of the genomic basis of adaptive variation; however, such resources are lacking for black spruce, with the few available being predominantly transcriptome-related. This thesis describes the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. To showcase the value of this new genomic resource, phylogenetic and comparative genomics analyses were performed. Phylogenetic trees were estimated from the nuclear and organelle genome sequences of P. mariana and five other spruces. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and three other taxa found in western North America, followed by the European P. abies. In contrast, mixed topologies with weaker statistical support were obtained in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these two genomes. Clustering of protein-coding sequences from the six Picea taxa and two Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive …
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/87059
note: THE GENOME OF BLACK SPRUCE: GENOME ANNOTATION & ANALYSES by Theodora Lo B.Sc., The University of British Columbia, 2020 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) December 2023 © Theodora Lo, 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: The Genome of Black Spruce: Genome Annotation & Analyses submitted by Theodora Lo in partial fulfilment of the requirements for the degree of Master of Science in Bioinformatics Examining Committee: Dr. Inanç Birol, Professor, Department of Medical Genetics, UBC Supervisor Dr. Joerg Bohlmann, Professor, Department of Botany, UBC Supervisory Committee Member Dr. Steven Hallam, Professor, Department of Microbiology & Immunology, UBC Supervisory Committee Member Dr. Marco Todesco, Assistant Professor, Department of Botany, UBC Additional Examiner iii Abstract Abiotic and biotic stresses associated with climate change have been identified as a dominant cause of forest tree mortality in boreal forests. Some tree populations may have the capacity for rapid adaptation or migration to keep pace with changing environmental conditions. One species of interest is black spruce (Picea mariana [Mill.] B.S.P.) as adaptive variation in relation to climate change has previously been reported for this transcontinental North American conifer. As exhibited in studies of other economically important forest trees, genomic resources play a critical role in advancing our understanding of the genomic basis of adaptive variation; however, such resources are lacking for black spruce, with the few available being predominantly transcriptome-related. This thesis describes the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold le…
has type: Thesis/Dissertation
date issued: 2024-05
is shown at: 10.14288/1.0438394
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: Birol, Inanc
type: Text
identifier URI: http://hdl.handle.net/2429/87059