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 Madagasc...

构建一个全面且有意义的系统发育假说，对于具有商业重要性的咖啡属（Coffea）而言，长期以来一直是咖啡研究者的核心目标。在分子研究中，进展因序列分歧度低而受限，导致系统发育树的拓扑分辨率和统计支持不足，尤其是对于主要支系以及马达加斯加分布的众多物种而言。本文报道了首个覆盖广泛样本、近乎完全解析的咖啡系统发育假说，该成果通过将基因型测序（GBS）技术与新开发的实验室工作流程相结合而获得——此流程可整合短读长下一代测序数据，用于少量额外样本的分析。生物地理格局表明，非洲或亚洲（或可能为阿拉伯半岛）是咖啡属起源最可能的祖先地，其在非洲、亚洲及西印度洋群岛（包括马达加斯加……）存在独立的辐射演化。