Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
Mol Phylogenet Evol. 2021 Jul;160:107118. doi: 10.1016/j.ympev.2021.107118. Epub 2021 Feb 18.
The genus Prunus, which contains 250-400 species, has ample genomic resources for the economically important taxa in the group including cherries, peaches, and almonds. However, the backbone of Prunus, specifically the position of the racemose group relative to the solitary and corymbose groups, remains phylogenetically uncertain. Surprisingly, phylogenomic analyses to resolve relationships in the genus are lacking. Here, we assemble transcriptomes from 17 Prunus species representing four subgenera, and use existing transcriptome assemblies, to resolve key relationships in the genus using a phylogenomic approach. From the transcriptomes, we constructed 21-taxon datasets of putatively single-copy nuclear genes with 591 and 379 genes, depending on taxon-occupancy filtering. Plastome sequences were obtained or assembled for all species present in the nuclear data set. The backbone of Prunus was resolved consistently in the nuclear and chloroplast phylogenies, but we found substantial cytonuclear discord within subgenera. Our nuclear phylogeny recovered a monophyletic racemose group, contrasting with previous studies finding paraphyly that suggests repeated allopolyploidy early in the evolutionary history of the genus. However, we detected multiple species with histories consistent with hybridization and allopolyploidy, including a deep hybridization event involving subgenus Amygdalus and the Armeniaca clade in subgenus Prunus. Analyses of gene tree conflict revealed substantial discord at several nodes, including the crown node of the racemose group. Alternative gene tree topologies that conflicted with the species tree were consistent with a paraphyletic racemose group, highlighting the complex reticulated evolutionary history of this group.
李属（Prunus）包含 250-400 个物种，其基因组资源丰富，包括樱桃、桃和杏仁等经济上重要的类群。然而，李属的骨干部分，特别是头状花序组相对于单生花序组和伞房花序组的位置，在系统发育上仍然不确定。令人惊讶的是，缺乏用于解析该属内关系的系统基因组分析。在这里，我们组装了代表四个亚属的 17 个李属物种的转录组，并使用现有的转录组组装，通过系统基因组学方法来解析该属中的关键关系。从转录组中，我们构建了包含 21 个分类群的数据集，其中包含了 591 个和 379 个基因，具体取决于分类群的占据过滤。所有存在于核数据集的物种都获得或组装了质体基因组序列。在核和质体系统发育中，李属的骨干部分得到了一致的解析，但我们在亚属内发现了大量的核质不和谐。我们的核系统发育恢复了一个单系的头状花序组，与以前的研究结果形成对比，这些研究结果表明属的早期进化历史中存在反复的异源多倍体化。然而，我们检测到多个具有与杂交和异源多倍体化一致历史的物种，包括涉及亚属杏仁和桃亚属 Armeniaca 分支的深层杂交事件。对基因树冲突的分析表明，在几个节点上存在大量的不和谐，包括头状花序组的冠节点。与种系发生树冲突的替代基因树拓扑结构与并系的头状花序组一致，突出了该组复杂的网状进化历史。
