Transcriptome assemblies of Cynanchum wilfordii and its related species (Apocynaceae).

objectivesCynanchum wilfordii is an important medicinal plant whose authenticated use is complicated by frequent adulteration with closely related species. Because genetic divergence among Cynanchum taxa is low, currently available molecular markers provide limited resolution. To address this challenge, we generated and analyzed transcriptome assemblies for C. wilfordii and related species, with the aim of identifying informative nuclear genes applicable to phylogenetic analyses and molecular marker development. DATA DESCRIPTION: Four RNA-seq libraries were generated from young leaf tissues of C. wilfordii, C. chinense, C. rostellatum, and Vincetoxicum floribundum, and sequenced on an Illumina NovaSeq 6000. Raw reads of C. auriculatum (re-identified as C. boudieri), a close relative of C. wilfordii, were also included. Clean reads were assembled de novo with Trinity, clustered into unigenes using CD-HIT-EST, and functionally annotated across multiple databases. Open reading frames were predicted with TransDecoder, and assembly quality was evaluated with BUSCO, using predicted mRNA transcripts from the Asclepias syriaca genome for comparison. Single-copy orthologues identified by OrthoFinder across six species were analyzed phylogenetically. These transcriptome data provide resources for identifying single- or low-copy nuclear genes useful in Apocynaceae phylogenetics and for developing molecular markers in C. wilfordii.