Transcriptome sequencing for twelve Caragana Species in China

We generated a full-length transcriptome of C. korshinskii and second-generation transcriptomes for 12 Caragana species collected from Inner Mongolia, Xinjiang, and Tibet. Based on the identified single-copy and one-to-one orthologous genes, we performed comparative transcriptomic analyses to reconstruct a robust phylogenetic tree, thereby elucidating the evolutionary relationships among these Caragana species. Evolutionary analyses identified positively selected genes and rapidly evolving genes associated with divergent adaptive strategies, including flowering phenology modulation, root system optimization, and reactive oxygen species scavenging. In addition, cuticular wax and cutin biosynthesis pathways were identified as conserved xeromorphic traits shared among multiple species. Furthermore, convergent evolution was observed in species occupying similar altitudinal and hydrothermal niches, as evidenced by parallel amino acid substitutions in C2H2, C3H, NAC, and mTERF transcription factor families.