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Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)

View ORCID ProfileKarolina Heyduk, View ORCID ProfileEdward V. McAssey, Jane Grimwood, Shengqiang Shu, Jeremy Schmutz, Michael R. McKain, Jim Leebens-Mack
doi: https://doi.org/10.1101/2020.06.14.150078
Karolina Heyduk
1School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
2Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
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  • For correspondence: heyduk@hawaii.edu
Edward V. McAssey
1School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
3Department of Biological Sciences, Quinnipiac University, Hamden, CT USA
4Department of Biology and Environmental Science, University of New Haven, West Haven, CT USA
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Jane Grimwood
5HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
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Shengqiang Shu
6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Jeremy Schmutz
5HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Michael R. McKain
7University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, USA
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Jim Leebens-Mack
8Department of Plant Biology, University of Georgia, Athens, GA USA
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Abstract

Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ~11kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from multiple accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case – Copia LTR transposons – did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. Further work will assess the degree to which transposon abundance and location has affected the epigenomic landscape, gene expression, and ecophysiology in Y. gloriosa.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 15, 2020.
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Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)
Karolina Heyduk, Edward V. McAssey, Jane Grimwood, Shengqiang Shu, Jeremy Schmutz, Michael R. McKain, Jim Leebens-Mack
bioRxiv 2020.06.14.150078; doi: https://doi.org/10.1101/2020.06.14.150078
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Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)
Karolina Heyduk, Edward V. McAssey, Jane Grimwood, Shengqiang Shu, Jeremy Schmutz, Michael R. McKain, Jim Leebens-Mack
bioRxiv 2020.06.14.150078; doi: https://doi.org/10.1101/2020.06.14.150078

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