Annotating and making use of the Avena sativa cv. Sang reference genome
Tsardakas Renhuldt, Nikos LU
(2023)
- Abstract
- Oats is an important cereal used for both food and feed. The topic of this thesis is the annotation of the genome of oat (Avena sativa) cv. Sang, as well as some of the things this genome and its annotation have been used for.
The first part of the thesis provides a short background to oat genomic resources, genomic resources in other plant species, and assembly of cereal genomes. Following this, it goes through the pipeline used to annotate the oat genome, covering various tools used, mentioning annotation pipelines used for other plant genomes, and comparing the results of cv. Sang annotation to annotations of other released oat genomes. It also briefly discusses a couple of tools used for functional annotation and... (More) - Oats is an important cereal used for both food and feed. The topic of this thesis is the annotation of the genome of oat (Avena sativa) cv. Sang, as well as some of the things this genome and its annotation have been used for.
The first part of the thesis provides a short background to oat genomic resources, genomic resources in other plant species, and assembly of cereal genomes. Following this, it goes through the pipeline used to annotate the oat genome, covering various tools used, mentioning annotation pipelines used for other plant genomes, and comparing the results of cv. Sang annotation to annotations of other released oat genomes. It also briefly discusses a couple of tools used for functional annotation and identification of homologous genes.
The following chapter looks at how this annotation may be used. It describes the pipeline used to identify homologous genes and provides an overview of how this was used to identify genes involved in epicuticular wax biosynthesis and in detoxification of Fusarium mycotoxins.
Use of genetic markers, including how they have already been used both to identify breeding barriers in oats, and to establish that this oat reference genome corresponds to cv. Sang are brought up in the next chapter. How the markers may be aligned to the genome and how they may be visualized are also discussed.
Next, mapping-by-sequencing is discussed, providing more details regarding the work done to identify the genes AsCer-q and AsGSK2.1. The method is explained, including selection of the number of individuals to include in the sequenced pools as well as the choices made to filter variants and genes. A background on the identified genes is also provided, before concluding with some thoughts regarding future work.
(Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/b78ea485-ea58-4b36-8451-2cb028e769b7
- author
- Tsardakas Renhuldt, Nikos
LU
- supervisor
-
- Nick Sirijovski LU
- Dag Ahrén LU
- Sofia Marmon LU
- Leif Bülow LU
- Bjorn Canback LU
- opponent
-
- Prof. Ingvarsson, Pär, Swedish University of Agricultural Sciences (SLU), Uppsala.
- organization
- publishing date
- 2023
- type
- Thesis
- publication status
- published
- subject
- keywords
- oats, Avena sativa, genomics, genome annotation, gene mapping, mapping-by-sequencing, brassinosteroids, Fusarium, genetic markers, GFViz, GSK3, UGT, cereals, epicuticular wax, plant genomics, marker visualization, AsGSK2.1, AsCer-q
- publisher
- Pure and Applied Biochemistry, Lund University
- defense location
- Lecture Hall KC:A, Kemicentrum, Naturvetarvägen 14, Faculty of Engineering LTH, Lund University, Lund
- defense date
- 2023-09-01 13:00:00
- ISBN
- 978-91-7422-966-0
- 978-91-7422-967-7
- language
- English
- LU publication?
- yes
- id
- b78ea485-ea58-4b36-8451-2cb028e769b7
- date added to LUP
- 2023-05-26 17:11:51
- date last changed
- 2023-10-24 03:12:06
@phdthesis{b78ea485-ea58-4b36-8451-2cb028e769b7,
abstract = {{Oats is an important cereal used for both food and feed. The topic of this thesis is the annotation of the genome of oat (<i>Avena sativa</i>) cv. Sang, as well as some of the things this genome and its annotation have been used for.<br/><br/>The first part of the thesis provides a short background to oat genomic resources, genomic resources in other plant species, and assembly of cereal genomes. Following this, it goes through the pipeline used to annotate the oat genome, covering various tools used, mentioning annotation pipelines used for other plant genomes, and comparing the results of cv. Sang annotation to annotations of other released oat genomes. It also briefly discusses a couple of tools used for functional annotation and identification of homologous genes.<br/><br/>The following chapter looks at how this annotation may be used. It describes the pipeline used to identify homologous genes and provides an overview of how this was used to identify genes involved in epicuticular wax biosynthesis and in detoxification of <i>Fusarium</i> mycotoxins.<br/><br/>Use of genetic markers, including how they have already been used both to identify breeding barriers in oats, and to establish that this oat reference genome corresponds to cv. Sang are brought up in the next chapter. How the markers may be aligned to the genome and how they may be visualized are also discussed. <br/><br/>Next, mapping-by-sequencing is discussed, providing more details regarding the work done to identify the genes <i>AsCer-q</i> and <i>AsGSK2.1</i>. The method is explained, including selection of the number of individuals to include in the sequenced pools as well as the choices made to filter variants and genes. A background on the identified genes is also provided, before concluding with some thoughts regarding future work. <br/>}},
author = {{Tsardakas Renhuldt, Nikos}},
isbn = {{978-91-7422-966-0}},
keywords = {{oats; Avena sativa; genomics; genome annotation; gene mapping; mapping-by-sequencing; brassinosteroids; Fusarium; genetic markers; GFViz; GSK3; UGT; cereals; epicuticular wax; plant genomics; marker visualization; AsGSK2.1; AsCer-q}},
language = {{eng}},
publisher = {{Pure and Applied Biochemistry, Lund University}},
school = {{Lund University}},
title = {{Annotating and making use of the <i>Avena sativa</i> cv. Sang reference genome}},
url = {{https://lup.lub.lu.se/search/files/147573918/e_spik_ex_Nikos.pdf}},
year = {{2023}},
}