Data from: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

长期以来，为具有商业重要性的咖啡属（Coffea）构建全面且可靠的系统发育假说，一直是咖啡研究人员的核心目标。在分子研究领域，序列分化程度偏低曾掣肘研究进展，导致系统发育树的拓扑分辨率与统计支持度不足，尤其针对主要演化支系以及马达加斯加境内的诸多物种。本研究首次报道了覆盖范围广泛、几乎完全解析的咖啡系统发育假说，该成果通过结合基因型分型测序（genotyping-by-sequencing, GBS）技术与全新开发的实验室流程实现，该流程可针对少量额外样本整合短读长下一代测序数据。生物地理模式显示，咖啡属起源的最可能祖先分布地为非洲、亚洲（或可能为阿拉伯半岛），且该属在非洲、亚洲以及西印度洋群岛（含马达加斯加与毛里求斯）发生了独立辐射演化。结合本研究构建的系统发育树，我们对咖啡因的演化展开了分析——咖啡因是对商业与社会具有重要意义的性状。仅在西非与中非赤道地区完全湿润环境中的咖啡物种内，检测到高且稳定的咖啡因含量，这可能是对更高虫害压力的适应性响应。然而，中等含量的咖啡因合成至少在距今200万至400万年前的一个马达加斯加演化支系中独立演化过一次，这表明要么咖啡属的早期演化历程中已具备咖啡因生物合成通路，要么咖啡属内的咖啡因合成存在趋同演化——这一现象与咖啡、茶与巧克力中的咖啡因合成趋同演化情况一致。