P. patens genomic and transcriptomic analyses
The model organism Physcomitrium patens, formerly Physcomitrella patens is a moss in the Funariaceae family. Due to P. patens ability to generate easily transgenic plants via homologous recombination, the interest of scientists worldwide was attracted. P. patens was the world's first complet...
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| Format: | Doctoral Thesis |
| Language: | English |
| Published: |
Philipps-Universität Marburg
2020
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| Online Access: | PDF Full Text |
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| Summary: | The model organism Physcomitrium patens, formerly Physcomitrella patens is a moss in the
Funariaceae family. Due to P. patens ability to generate easily transgenic plants via homologous
recombination, the interest of scientists worldwide was attracted. P. patens was the world's first
completely sequenced non-seed plant genome (V1). Constant improvements of the genome assembly
and the associated gene annotations resulted in the current P. patens pseudo-chromosomal genome
version (V3). This genome version is the basis of all analyses performed in this thesis.
Since P. patens became a U.S. Department of Energy Joint Genome Institute (DOE JGI) plant flagship
genome 1 and a member of the JGI Gene Atlas project 2, hundreds of P. patens RNA-seq samples were
generated. During my time as a PhD student, I analysed the JGI Gene Atlas RNA-seq samples and
several dozen other RNA-seq samples from different projects. These RNA-seq samples contained data
from five different P. patens ecotypes/accessions (Gransden, Kaskaskia, Reute, Villersexel, and
Wisconsin).To efficiently analyse this data, I developed a powerful RNA-seq pipeline to perform
differentially expressed gene (DEG) calling. The performance of the RNA-seq pipeline was tested by
comparing its results to commercial software solutions and multiple RNA-seq samples from different
species.
My newly generated gene expression results, together with previous published expression data from
a variety of other projects, were stored at our novel online tool PEATmoss. Furthermore, my gene
version lookup tables were implemented in a database structure. This, allows PEATmoss users to find
gene models of different gene annotation versions and to use them in PEATmoss.
With an updated version of my RNA-seq pipeline, I identified and analysed sequence variations in P.
patens accessions. A clear clustering by individual accessions could be shown. I could demonstrate,
that due to decades of vegetative propagation in laboratories, somatic mutations have accumulated
in Gransden laboratory plants. In addition, we used restriction fragment length polymorphism (RFLP)
to offer a simple method for quick identification of unknown P. patens plants.
1 https://jgi.doe.gov/our-science/science-programs/plant-genomics/plant-flagship-genomes/
2 https://jgi.doe.gov/doe-jgi-plant-flagship-gene-atlas/ |
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| Physical Description: | 153 Pages |
| DOI: | 10.17192/z2020.0463 |