Transcriptome assembly used in the paper: "The endomicrobiome and weed invasiveness in Mediterranean ecosystems"

Mediterranean ecosystems, one of the most significant global hotspots of biodiversity, are threatened by invasive weeds. Although endomicrobiomes – the vast array of microbes colonising living plant tissues – are known to affect plant fitness, their contribution to weed invasiveness remains virtually unknown. Here we experimentally assessed the role of the<b> </b>endomicrobiome in the microevolution of <i>Taraxacum</i> <i>officinale</i> (common dandelion), a widespread invasive weed in Mediterranean ecosystems worldwide. In a culling experiment across five generations, we compared the microevolutionary rates of <i>T. officinale</i> from Mediterranean ecosystems on five continents grown with intact or reduced native seed-borne endomicrobiomes. Additionally, we conducted a competition experiment with F₁ and F₅ individuals to assess their impacts on native local Asteraceae species. We found <i>T. officinale</i> individuals growing with their intact endomicrobiomes to exhibit faster and more positive trait evolution than individuals growing with reduced endomicrobiomes. Enhanced competitiveness of endomicrobiome-colonized <i>T. officinale </i>plants<i> </i>with local Asteraceae species was apparently caused by increased synthesis of allelochemicals in shoots and rhizosphere soil, with gene expression analyses also showing the endomicrobiome to affect the expression by <i>T. officinale</i> of stress response and RNA-directed DNA methylation genes. Our findings provide novel insights into the mechanisms underlying weed invasiveness in Mediterranean ecosystems, highlighting the endomicrobiome as a potent driving force in the evolutionary processes associated with plant invasion success.

地中海生态系统作为全球最重要的生物多样性热点区域之一，正受到入侵杂草的威胁。尽管定殖于活植物组织的各类微生物（endomicrobiome）已知会影响植物适合度，但它们对杂草入侵性的贡献几乎仍未被探明。本研究通过实验评估了植物内生微生物组在西洋蒲公英（Taraxacum officinale，俗称普通蒲公英）微进化过程中的作用——该物种是全球地中海生态系统中广泛分布的入侵杂草。我们开展了为期五代的微生物组剔除实验，比较了来自全球五大洲地中海生态系统的西洋蒲公英，在保留完整原生种子携带内生微生物组与降低原生种子携带内生微生物组丰度两种条件下的微进化速率。此外，我们利用子一代（F₁）与子五代（F₅）个体开展了竞争实验，以评估其对本地土著菊科物种的影响。研究发现，保留完整内生微生物组的西洋蒲公英个体，其性状进化速率更快、进化方向更趋正向，优于内生微生物组丰度被降低的个体。携带完整内生微生物组的西洋蒲公英植株，对本地菊科物种的竞争能力显著提升，这一现象显然源于其地上组织与根际土壤中化感物质合成量的增加；基因表达分析亦显示，内生微生物组可调控西洋蒲公英的胁迫响应基因与RNA指导的DNA甲基化基因的表达。本研究结果为解析地中海生态系统中杂草入侵的内在机制提供了全新视角，同时凸显了内生微生物组作为植物入侵成功相关进化过程的强效驱动因素的重要作用。