Chloroplast primers for clade-wide phylogenetic studies of Thalictrum

Abstract

Premise: Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). Methods and Results: We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly assembled plastomes and one previously sequenced plastome, we designed and validated 28 primer pairs to target variable portions of the chloroplast genome in Thalictrum. Furthermore, we tested the validated primers in 62 species of Thalictrum. The total alignment length of the 28 regions was 15,268 bp with 2443 variable sites and 92% character occupancy. Conclusions: The newly developed chloroplast primer pairs improve the phylogenetic resolution (bootstrap support and tree certainty) in Thalictum and will be a useful resource for future phylogenetic and evolutionary studies for species in the genus and in close relatives in Thalictroideae.