Data from: Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)

Background: Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a polyploid complex formed through unidirectional (and, in the first two cases, recurrent) hybridization between the widespread diploids D. fuchsii and D. incarnata. Differing considerably in geographical extent and ecological tolerance, the three allopolyploids together provide a useful system to explore genomic responses to allopolyploidization and reveal their role in adaptation to contrasting environments. Results: Analyses of cDNA-AFLPs show a significant increase in the range of gene expression of these allopolyploid lineages, demonstrating higher potential for phenotypic plasticity than shown by either parent. Moreover, allopolyploid individuals express significantly more gene variants (including novel alleles) than their parents, providing clear evidence for an increase in biological complexity following allopolyploidization. Significantly more genetic mutations have accumulated in the older D. majalis compared with the younger D. traunsteineri since their respective formation. Conclusions: Multiple origins of these tetraploids contribute to differential patterns of gene expression with a distinct geographic structure. However, several transcripts conserved within each allopolyploid taxon differ between taxa, indicating that habitat preferences shape similar expression patterns in these independently formed allopolyploids. Statistical signals separate several adaptive transcripts, related mainly to a combination of water availability and temperature that may play a role favouring the persistence of individuals in their native environments. In addition to stabilizing the allopolyploid genome, genetic and epigenetic alterations are key determinants of the adaptive success of the new polyploid species after recurrent allopolyploidization events, potentially triggering reproductive isolation between the resulting lineages.背景：杂交与多倍化是驱动植物演化与适应的关键驱动力，长期持续地推动植物进化进程。掌兰属（Dactylorhiza）的D. majalis s.s.、D. traunsteineri s.l. 与D. ebudensis均为某一多倍体复合群中的三个异源多倍体（allopolyploid）物种，其起源均为广泛分布的二倍体物种D. fuchsii与D. incarnata之间的单向杂交（其中前两个物种的杂交事件甚至多次重复发生）。这三个异源多倍体物种在地理分布范围与生态耐受特性上存在显著差异，共同构成了探究异源多倍化后的基因组响应、并揭示其在迥异环境适应中作用的理想实验体系。 结果：互补DNA扩增片段长度多态性（cDNA-AFLPs）分析显示，这些异源多倍体谱系的基因表达范围显著扩大，展现出相较于双亲更高的表型可塑性（phenotypic plasticity）潜力。此外，异源多倍体个体所表达的基因变异（包括新型等位基因）数量显著多于亲本物种，清晰证实异源多倍化后生物复杂度显著提升。值得注意的是，相较于形成时间较晚的D. traunsteineri，起源更早的D. majalis自其形成以来积累了更多的遗传突变。 结论：这些四倍体物种的多次独立起源，造就了具有显著地理结构特征的基因表达分化模式。不过，各异源多倍体类群内部保守的若干转录本在类群间存在差异，这暗示生境偏好塑造了这些独立起源的异源多倍体的相似表达模式。统计分析筛选出若干适应性转录本，其表达主要与水分有效性及温度的组合效应相关，或有助于这些物种在原生境中维持种群存续。除了稳定异源多倍体基因组之外，遗传与表观遗传改变亦是多次异源多倍化事件后新生多倍体物种适应性成功的关键决定因素，甚至可能引发衍生谱系间的生殖隔离。