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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

Kim A. Steige, Johan Reimegård, Carolin A. Rebernig, Claudia Köhler, Douglas G. Scofield, View ORCID ProfileTanja Slotte
doi: https://doi.org/10.1101/044016
Kim A. Steige
1Dept. of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, 75236 Uppsala, SWEDEN
2Science for Life Laboratory, Dept. of Ecology, Environment and Plant Sciences, Stockholm University, SE-10691 Stockholm, SWEDEN
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Johan Reimegård
3Science for Life Laboratory, Dept. of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, SWEDEN
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Carolin A. Rebernig
4Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, SWEDEN
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Claudia Köhler
4Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, SWEDEN
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Douglas G. Scofield
1Dept. of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, 75236 Uppsala, SWEDEN
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Tanja Slotte
1Dept. of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, 75236 Uppsala, SWEDEN
2Science for Life Laboratory, Dept. of Ecology, Environment and Plant Sciences, Stockholm University, SE-10691 Stockholm, SWEDEN
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  • ORCID record for Tanja Slotte
  • For correspondence: Tanja.Slotte@su.se
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Abstract

The formation of an allopolyploid species involves the merger of two genomes with separate evolutionary histories. In allopolyploids, genes derived from one progenitor species are often expressed at higher levels than those from the other progenitor. It has been suggested that this could be due to differences in transposable element (TE) content among progenitors, as silencing of TEs can affect expression of nearby genes. Here, we examine the role of TEs for expression biases in the widespread allotetraploid Capsella bursa-pastoris and in diploid F1 hybrids generated by crossing Capsella orientalis and Capsella rubella, two close relatives of the progenitors of C. bursa-pastoris. As C. rubella harbors more TEs than C. orientalis, we expect C. orientalis alleles to be expressed at higher levels if TE content is key for expression biases. To test this hypothesis, we quantified expression biases at approximately 5800 genes in flower buds and leaves, while correcting for read mapping biases using genomic data. While three of four C. bursa-pastoris accessions exhibited a shift toward higher relative expression of C. orientalis alleles, the fourth C. bursa-pastoris accession had the opposite direction of expression bias, as did diploid F1 hybrids. Associations between TE polymorphism and expression bias were weak, and the effect of TEs on expression bias was small. These results suggest that differences in TE content alone cannot fully explain expression biases in these species. Future studies should investigate the role of differences in TE silencing efficacy, as well as a broader set of other factors. Our results are important for a more general understanding of the role of TEs for cis-regulatory evolution in plants.

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Posted March 16, 2016.
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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
Kim A. Steige, Johan Reimegård, Carolin A. Rebernig, Claudia Köhler, Douglas G. Scofield, Tanja Slotte
bioRxiv 044016; doi: https://doi.org/10.1101/044016
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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
Kim A. Steige, Johan Reimegård, Carolin A. Rebernig, Claudia Köhler, Douglas G. Scofield, Tanja Slotte
bioRxiv 044016; doi: https://doi.org/10.1101/044016

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