| dc.contributor.advisor | Macas, Jiří | |
| dc.contributor.author | Vondrak, Tihana | |
| dc.date.accessioned | 2025-03-06T08:58:19Z | |
| dc.date.available | 2025-03-06T08:58:19Z | |
| dc.date.issued | 2022 | |
| dc.date.submitted | 2022-07-11 | |
| dc.identifier.uri | https://dspace.jcu.cz/handle/20.500.14390/46833 | |
| dc.format | 145 | |
| dc.format | 145 | |
| dc.language.iso | eng | |
| dc.publisher | Jihočeská univerzita | cze |
| dc.rights | Bez omezení | |
| dc.title | Assembly and analysis of repeat-rich regions of plant genomes | cze |
| dc.title.alternative | Analysis of repeat-rich regions of plant genomes using long read sequencing technologies | eng |
| dc.type | disertační práce | cze |
| dc.identifier.stag | 55944 | |
| dc.description.abstract-translated | Satellite DNA has been identified in varying proportions in many eukaryotic genomes. It consists of monomeric units arranged in tandem into long, homogeneous arrays. Due to its repetitive nature, satellite DNA is difficult to assemble and analyze, and has therefore been largely neglected in research. With the development of next generation sequencing technologies such as Illumina, research on satellite DNA has intensified and our understanding of it has improved. However, the information we obtain with Illumina reads is limited by their short length. While we can characterize the sequence of satellite DNA and its abundance in genomes, it is not possible to study the long-range organization of satellite DNA, which limits our understanding of the origin
and evolution of satellite DNA. This limitation can be addressed by using the latest generation of sequencing technologies that generate much longer reads of tens to hundreds of kilobases.
The goal of this work was to develop bioinformatics approaches for analyzing the properties of satellite DNA arrays from long sequence reads or from genome assemblies generated with these reads. These were then used to analyze populations of satellite repeats throughout the genome or in the specific type of chromatin in three plant species that differ in the organization of their centromeres. | eng |
| dc.date.accepted | 2022-09-15 | |
| dc.description.department | Přírodovědecká fakulta | cze |
| dc.thesis.degree-discipline | Molecular and Cell Biology and Genetics | cze |
| dc.thesis.degree-grantor | Jihočeská univerzita. Přírodovědecká fakulta | cze |
| dc.thesis.degree-name | Ph.D. | |
| dc.thesis.degree-program | Molecular and Cell Biology | cze |
| dc.description.grade | Dokončená práce s úspěšnou obhajobou | cze |
| dc.contributor.referee | Hřibová, Eva | |
| dc.contributor.referee | Schneeweiss, Hanna | |
| dc.description.defence | <p>Tihana Vondrak PhD defence, 15th September 2022<br />
"Analysis of repeat-rich regions of plant genomes using long-read sequencing technologies"</p>
<p>Ph.D. mentor: RNDr. Jiri Macas, Ph.D., comittee: prof. RNDr. Frantisek Marec,CSc. (head), doc. David Kopecky, Ph.D., RNDr. Petr Nguyen, Ph.D., Mgr. Iva Mozgova, Ph.D., opponents: Mgr. Eva Hribova, Ph.D., Univ. Prof. Mag. Dr. Hanna Schneeweiss.</p>
<p>The mentor read Ph.D. candidate evaluation. The Ph.D. candidate presented their project in time limit 30 minutes. </p>
<p>The opponents read their reviews and they expressed their great satisfaction with the quality of the thesis. The Ph.D. candidate discussed the questions with the opponents. </p>
<p>Q: Are the centromeric regions from the holocentric chromosomes recombining?<br />
Q: Is there any tool to de novo recognize tandem repeats in the Nanopore reads?<br />
Q: What is the general error rate for the Oxford Nanopore reads?</p>
<p>The head of the comittee opened the discussion from the comitee.</p>
<p>Q: Is there any relationship between chromosome number/size and recombination rate?<br />
Q: How do you know certain region has centromeric activity?<br />
Q: Do the short arrays have higher rate of truncation?<br />
Q: Did you identifiy some satelites which can be used as a markers do distinguish certain in plants? </p>
<p>The Ph.D. candidate answered all the question and the comittee was satisfied with the discussion. </p>
<p>All committee members including opponents, voted in presence:</p>
<p>6 votes polled, 6 votes valid, 6 votes passed, 0 votes failed </p>
<p> </p> | cze |
