Pentatricopeptide proteins as tools for chloroplast engineering in Marchantia polymorpha
type: CreativeWork
description: Marchantia polymorpha is a liverwort, one of the early-diverging groups of land plants, and has seen a renaissance as a model plant system in recent years as a result of access to a range of powerful tools for genome engineering both at the nuclear and chloroplast level. Along with rapid regeneration that enables the facile generation of large numbers of nuclear-transformants, and rapid progression to homoplasmy during chloroplast transformation. Additionally, its planar morphology is particularly suited to microscopic analysis, especially of subcellular compartments. In this thesis I validated a pipeline for genome assembly refinement using short-read sequencing data in combination with high-quality reference sequences, to produce an updated version of the nuclear genomes for the Cam accession of M. polymorpha. The Cam accession is particularly well suited to chloroplast transformation due to the ease with which spores can be generated to use in the biolistic delivery of DNA. I then demonstrated a substantial improvement in genome contiguity for the Cam nuclear genomes compared to previous versions, resulting in an increase in genome coverage of ~21.5% for both Cam-1 and Cam-2, particularly from a large increase in repeat content. The updated Cam genomes were then used to perform a large-scale analysis of pentatricopeptide repeat proteins (PPR) in M. polymorpha. The PPR proteins are a group of nuclear-encoded RNA-binding proteins that have seen a significant expansion in land plants, and which localise to the chloroplasts and mitochondria to facilitate organellar gene expression. The results indicated that M. polymorpha PPR genes are intron rich, containing on average 4 introns each, this was in contrast to the PPR genes of flowering plants which are predominantly intron-less as a result of recent expansion through retrotransposition, suggesting that the M. polymorpha PPR genes have an ancient origin. Analysis was performed on multiple RNA-seq data sets from differ…
abstract: Marchantia polymorpha is a liverwort, one of the early-diverging groups of land plants, and has seen a renaissance as a model plant system in recent years as a result of access to a range of powerful tools for genome engineering both at the nuclear and chloroplast level. Along with rapid regeneration that enables the facile generation of large numbers of nuclear-transformants, and rapid progression to homoplasmy during chloroplast transformation. Additionally, its planar morphology is particularly suited to microscopic analysis, especially of subcellular compartments. In this thesis I validated a pipeline for genome assembly refinement using short-read sequencing data in combination with high-quality reference sequences, to produce an updated version of the nuclear genomes for the Cam accession of M. polymorpha. The Cam accession is particularly well suited to chloroplast transformation due to the ease with which spores can be generated to use in the biolistic delivery of DNA. I then demonstrated a substantial improvement in genome contiguity for the Cam nuclear genomes compared to previous versions, resulting in an increase in genome coverage of ~21.5% for both Cam-1 and Cam-2, particularly from a large increase in repeat content. The updated Cam genomes were then used to perform a large-scale analysis of pentatricopeptide repeat proteins (PPR) in M. polymorpha. The PPR proteins are a group of nuclear-encoded RNA-binding proteins that have seen a significant expansion in land plants, and which localise to the chloroplasts and mitochondria to facilitate organellar gene expression. The results indicated that M. polymorpha PPR genes are intron rich, containing on average 4 introns each, this was in contrast to the PPR genes of flowering plants which are predominantly intron-less as a result of recent expansion through retrotransposition, suggesting that the M. polymorpha PPR genes have an ancient origin. Analysis was performed on multiple RNA-seq data sets from differ…
author: Boxall, WT
language: eng
keywords: Biolistics, Chloroplast, Marchantia, Marchantia polymorpha, Pentatricopeptide, Plastid, PPR
license: https://www.repository.cam.ac.uk/bitstreams/8be882b0-031c-4d35-8b27-5be98d117089/download
license: http://purl.org/NET/rdflicense/allrightsreserved
date published: 2025-03-31
date modified: 2026-07-22T22:24:28Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.123109