The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

中文翻译：

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使用系统基因组学和基因组大小估计解开疫霉属中的杂交

疫霉属包括许多经济上和生态上重要的植物病原体。先前已在 12 个系统发育进化枝中的至少 6 个中鉴定出杂交种。与它们的祖先相比，这些杂种可能会感染更广泛的宿主范围并显示出增强的活力。因此，疫霉属杂交种对农业和自然生态系统构成严重威胁。因此，早期和正确鉴定杂种对于充分保护植物是必不可少的，但这受到形态学和传统分子方法的局限性的阻碍。杂交体的鉴定在进化研究中也很重要，因为杂交体在系统发育树中的定位可能导致次优拓扑。为了改进杂交种的鉴定，我们对 614 个疫霉属分离株的全属集合进行了基因分型测序 (GBS) 和基因组大小估计。基于基因座和等位基因计数的分析，尤其是基于物种特异性基因座和基因组大小估计的组合，使我们能够确认和表征 27 个先前描述的杂交物种，并发现 16 个新的杂交物种。我们的方法对于以前所未有的分辨率进行物种鉴定也很有价值，并进一步允许正确命名错误鉴定的分离株。我们使用基于串联和聚结的系统发育方法，使用 140 个非杂交疫霉分离株的 GBS 数据构建可靠的系统发育。杂种物种随后在这棵系统发育树中与它们的祖先相连。