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Cis-regulatory variation and allele-specific expression in the collared flycatcher (Ficedula albicollis) genome
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-384392OAI: oai:DiVA.org:uu-384392DiVA, id: diva2:1320457
Available from: 2019-06-04 Created: 2019-06-04 Last updated: 2019-06-11
In thesis
1. Gene regulatory evolution in flycatchers: statistical approaches for the analysis of allele-specific expression
Open this publication in new window or tab >>Gene regulatory evolution in flycatchers: statistical approaches for the analysis of allele-specific expression
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the molecular mechanisms underlying evolutionary changes in gene expression is a major research topic in biology. While a powerful approach to study this is the analysis of allele-specific expression (ASE), most of previously published methods can only be applied to lab organisms. In this thesis, to enable the analysis of ASE in natural organisms, I developed two methods for ASE detection. The first one was Bayesian negative binomial approach, and the second one was Read-backed Phasing-based ASE approach. Both methods performed well in simulations and comparisons. By applying those methods, I found that ASE was prevalent in natural flycatcher species. Combining the analyses of differential gene expression and ASE, I found a widespread cis-trans compensation and a critical role of tissue-specific regulatory mechanism during gene expression evolution. Moreover, for cis-regulatory sequences, there was a larger proportion of slightly deleterious mutations and weaker signatures of positive selection for genes with ASE than genes without ASE. For coding sequence, no such difference was observed. These results indicated that the evolution of gene expression and coding sequences could be uncoupled and occurred independently.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 46
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1823
Keywords
ASE, gene expression evolution, bayesian, RPASE, flycatcher.
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-384493 (URN)978-91-513-0686-5 (ISBN)
Public defence
2019-09-04, Lindahlsalen, Norbyvägen 14, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-08-13 Created: 2019-06-05 Last updated: 2019-08-13

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Citation style
  • apa
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Output format
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