Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae)

Frontiers in Plant Science

卷:11

Michael R. McKain²  Edward V. McAssey³  Karolina Heyduk⁴  Jim Leebens-Mack⁵  Jane Grimwood⁶  Jeremy Schmutz⁷  Shengqiang Shu⁷ 

[1] Department of Biological Sciences, Quinnipiac University, Hamden, CT, United States;

[2] Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States;

[3] Department of Biology and Environmental Science, University of New Haven, West Haven, CT, United States;

[4] Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States;

[5] Department of Plant Biology, University of Georgia, Athens, GA, United States;

[6] HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States;

[7] Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States;

[8] School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States;

关键词: homoploid;    hybrid;    Yucca;    chloroplast;    transposable element;    genomic shock;   

DOI  :  10.3389/fpls.2020.573767

来源: DOAJ

【 摘 要 】

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 ∼11 kb 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 41 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. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.

【 授权许可】

Unknown