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Identification and large-scale analysis of retrogenes in animal genomes

Michał Kabza

Abstract

In my PhD thesis I focused on the large–scale identification of retrocopies in animal genomes and the analysis of their potential functionality, as well as on the evolutionary events affecting retrocopy repertoire in human genomes. In the first publication I present RetrogeneDB, a new database containing retrocopy annotations. Unlike previous similar databases, such as HOPPSIGEN or RCPedia, RetrogeneDB is not limited to model organisms and contains retrocopy predictions for 62 animal genomes downloaded from Ensembl 73 databases. RetrogeneDB is currently located at http://retrogenedb.amu.edu.pl and overall contains 84 808 retrocopies, 64 225 of which are not annotated in the Ensembl databases. The second publication forming the basis of my PhD thesis describes the analysis of inter–population differences in retrocopy repertoire and expression. In contrast to previous studies, mostly focused on detection of novel retroposition events, my primal goal was to detect the loss of ancestral, functional retrocopies (retrogenes) in different human populations.
Record ID
UAMdb57d43e982d4b05a6b3c5f4eee1ab1c
Diploma type
Doctor of Philosophy
Author
Title in Polish
Identyfikacja i wielkoskalowa analiza retrogenów w genomach zwierzęcych
Title in English
Identification and large-scale analysis of retrogenes in animal genomes
Language
eng (en) English
Certifying Unit
Faculty of Biology (SNP/WB/FoB) [Not active]
Discipline
biotechnology / (biological sciences domain) / (biological sciences)
Status
Finished
Year of creation
2016
Start date
28-11-2014
Defense Date
08-11-2016
Title date
25-11-2016
Supervisor
Keywords in English
inter-population differences
Abstract in English
In my PhD thesis I focused on the large–scale identification of retrocopies in animal genomes and the analysis of their potential functionality, as well as on the evolutionary events affecting retrocopy repertoire in human genomes. In the first publication I present RetrogeneDB, a new database containing retrocopy annotations. Unlike previous similar databases, such as HOPPSIGEN or RCPedia, RetrogeneDB is not limited to model organisms and contains retrocopy predictions for 62 animal genomes downloaded from Ensembl 73 databases. RetrogeneDB is currently located at http://retrogenedb.amu.edu.pl and overall contains 84 808 retrocopies, 64 225 of which are not annotated in the Ensembl databases. The second publication forming the basis of my PhD thesis describes the analysis of inter–population differences in retrocopy repertoire and expression. In contrast to previous studies, mostly focused on detection of novel retroposition events, my primal goal was to detect the loss of ancestral, functional retrocopies (retrogenes) in different human populations.
Thesis file
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Uniform Resource Identifier
https://researchportal.amu.edu.pl/info/phd/UAMdb57d43e982d4b05a6b3c5f4eee1ab1c/
URN
urn:amu-prod:UAMdb57d43e982d4b05a6b3c5f4eee1ab1c

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