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.

植物中的杂交会导致表型和基因型扰动，会对混合生理，生态学和整体适应性产生巨大影响。杂交也会干扰转座因子的表观遗传控制，导致它们的增殖。对杂交后维持基因组完整性的机制的理解常常与杂种植物物种中倍性的变化混淆。相对于其亲本，染色体数目没有变化的同倍体杂种，提供了研究在没有倍性变化的情况下杂交的基因组后果的机会。丝兰 （天门冬科）是一种年轻的单倍体杂种，由 丝兰 和 丝兰丝兰。 先前对约11 kb的叶绿体基因组和核编码微卫星的分析涉及单个 黄叶耶氏酵母 基因型作为...的母体 Y. gloriosa。 使用全基因组重测序，我们组装了来自所有三个物种的41个种的叶绿体基因组，以重新评估杂种的杂种起源。 耶氏酵母。我们进一步使用重测序数据来注释这三个物种中的转座子丰度，并使用mRNA序列分析转座子的转录。叶绿体的系统发育和单倍型分析表明，多种杂交事件有助于起源。耶氏酵母，两个亲本物种都作为母体供体。这三个物种在超家族水平上的转座子丰度明显不同。杂种在TE超家族的丰富度中经常居于亲本物种的中间，或者看起来更像一个或另一个亲本。仅在一种情况下-科皮亚 LTR转座子—已完成 耶氏酵母相对于父母双方而言，丰度要高得多。这三个物种的表达模式显示转座子的转录活性几乎没有增加，表明在该物种中没有发生转座子释放耶氏酵母杂交后，或通过杂交激活的任何转座子迅速沉默。转座子家族的鉴定和定量以及表达证据为寻求将表观遗传学与同倍体杂交系统中重要的性状变异联系起来的其他工作铺平了道路。