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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
Uppsala University, Science for Life Laboratory, SciLifeLab.
Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala.
Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala.
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(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-268925OAI: oai:DiVA.org:uu-268925DiVA: diva2:881802
Available from: 2015-12-11 Created: 2015-12-11 Last updated: 2016-02-12
In thesis
1. Cis-regulatory variation and divergence in Capsella
Open this publication in new window or tab >>Cis-regulatory variation and divergence in Capsella
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cis-regulatory changes in e.g. promoters or enhancers that affect the expression of a linked focal gene have long been thought to be important for adaptation. In this thesis, I investigate the selective importance and genomic correlates of cis-regulatory variation and divergence in the genus Capsella, using massively parallel sequencing data. This genus provides an opportunity to investigate cis-regulatory changes in response to polyploidization and mating system shifts, as it harbors three diploid species, the outcrosser Capsella grandiflora and the selfers Capsella orientalis and Capsella rubella, as well as the tetraploid Capsella bursa-pastoris. We first identify cis-regulatory changes associated with adaptive floral evolution in connection with the recent switch to self-fertilization in C. rubella and show that cis-regulatory changes between C. rubella and its outcrossing close relative C. grandiflora are associated with differences in transposable element content. Second, we show that variation in positive and purifying selection is important for the distribution of cis-regulatory variation across the genome of C. grandiflora. Interestingly, the presence of polymorphic transposable elements is strongly associated with cis-regulatory variation in C. grandiflora. Third, we show that the tetraploid C. bursa-pastoris is of hybrid origin and investigate the contribution of both parental species to gene expression. We show that gene expression in the tetraploid is partly explained by cis-regulatory divergence between the parental species. Nonetheless, within C. bursa-pastoris there is a great deal of variation in homeolog expression. In summary, this thesis explores the role of cis-regulatory changes for adaptive morphological changes in connection to a shift in mating system, the role of cis-regulatory divergence between progenitor species for an allopolyploid as well as the impact of positive and purifying selection on cis-regulatory variation within a species.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 45 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1332
Keyword
Capsella, Shepherd's Purse, cis-regulatory changes, allele-specific expression, mating system shift, floral evolution, polyploidy, positive selection, purifying selection, transposable elements, small RNA, methylation, transposable element silencing, distribution of fitness effects
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-268953 (URN)978-91-554-9442-1 (ISBN)
Public defence
2016-02-15, Lindahlsalen, Norbyvägen 18 A, Uppsala, 13:15 (English)
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Supervisors
Available from: 2016-01-22 Created: 2015-12-11 Last updated: 2016-02-12

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Steige, Kim A.

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