Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

Phylogenetic relationships are hotspots for orchid studies with controversial standpoints. Traditionally, the phylogenies of orchids are based on morphology and subjective factors. Although more reliable than classic phylogenic analyses, the current methods are based on a few gene markers and PCR amplification, which are labor intensive and cannot identify the placement of some species with degenerated plastid genomes. Therefore, a more efficient, labor-saving and reliable method is needed for phylogenic analysis. Here, we present a method of orchid phylogeny construction using transcriptomes. Ten representative species covering five subfamilies of Orchidaceae were selected, and 315 single-copy orthologous genes extracted from the transcriptomes of these organisms were applied to reconstruct a more robust phylogeny of orchids. This approach provided a rapid and reliable method of phylogeny construction for Orchidaceae, one of the most diversified family of angiosperms. We also showed the rigorous systematic position of holomycotrophic species, which has previously been difficult to determine because of the degenerated plastid genome. We concluded that the method presented in this study is more efficient and reliable than methods based on a few gene markers for phylogenic analyses, especially for the holomycotrophic species or those whose DNA sequences have been difficult to amplify. Meanwhile, a total of 315 single-copy orthologous genes of orchids are offered and more informative loci could be used in the future orchid phylogenetic studies.

兰科植物的系统发育关系（phylogenetic relationships）是兰花研究的热点领域，且长期存在诸多争议观点。传统兰花系统发育研究多基于形态学特征与主观因素。尽管相较于经典系统发育分析，当前主流方法的可靠性有所提升，但这类方法仍依赖少数基因标记与聚合酶链式反应（PCR）扩增，不仅劳动强度大，且无法准确鉴定部分质体基因组退化物种的系统发育位置。因此，亟需一种更高效、省力且可靠的系统发育分析方法。本研究提出一种基于转录组（transcriptome）的兰科（Orchidaceae）系统发育构建方法。我们选取了覆盖兰科5个亚科的10个代表性物种，从其转录组中提取得到315个单拷贝直系同源基因（single-copy orthologous genes），以此构建了更为稳健的兰科系统发育树。兰科是被子植物（angiosperms）中物种多样性最高的类群之一，本方法为其系统发育研究提供了一种快速可靠的技术路径。针对此前因质体基因组退化而难以确定系统分类地位的全真菌营养型物种（holomycotrophic species），本研究明确了其严谨的系统位置。研究结果表明，相较于基于少数基因标记的传统系统发育分析方法，本研究所提出的方法在效率与可靠性上更具优势，尤其适用于全真菌营养型物种或难以扩增DNA序列的类群。此外，本研究共提供了315个兰花单拷贝直系同源基因位点，未来可将更多信息丰富的基因座应用于兰科系统发育相关研究中。