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Genus  Rubus  represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera ( Chamaebatus ,  Idaoeobatus , and  Malochobatus ). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the  Rubus  species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic  Rubus  species: subg.  Idaeobatus  ( R .  glandulosopunctatus ,  R .  incanus ,  R .  parviaraliifolius ,  R rubroangustifolius ,  R .  taitoensis,  and  R .  taiwanicolus ) and subg.  Malachobatus  ( R .  kawakamii  and  R .  laciniastostipulatus ) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions ( rps16 / trnQ ,  petA / psbJ ,  rpl32 / trnL -UAG, and  trnT -UGU/ trnL -UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within  Rubus  in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.

Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan