Abstract
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.
Highlights
Taiwan originates from the continental Taiwan-Ryukyu Archipelago, lying on the western rim of the Pacific Ocean approximately 150 km from the southeastern coast of China, separated by the Taiwan Strait
Few other endemic species of Rubus belong to subgenus Chamaebatus, we were not able to include any representatives in current study
The size of complete plastome sequences ranged from 155,566 bp (R. rubroangustifolius) to 156,236 bp (R. laciniatostipulatus)
Summary
Taiwan originates from the continental Taiwan-Ryukyu Archipelago, lying on the western rim of the Pacific Ocean approximately 150 km from the southeastern coast of China, separated by the Taiwan Strait. 41 species from three subgenera are currently recognized in Taiwan; i.e., Chamaebatus (3 species), Idaoeobatus (27 species), and Malochobatus (11 species) Among these species, approximately 40% (15 species) are considered endemic to Taiwan, while the remaining species occur in mainland China (23 species; 57.5%), Japan (12 species; 30%), and the Philippines (6 species; 15%)[17]. Since the first report of three partial Rubus plastomes being part of the Rosaceae phylogeny[33], several complete chloroplast genomes belonging to different subgenera, i.e., Anoplobatus and Idaeobatus, have been recently reported, and useful hotspot regions for phylogenetic analysis have been s uggested[34,35,36,37,38,39]. The results from this study will aid in the development of useful chloroplast markers from hotspot regions, facilitating increased resolution of phylogenetic relationships among closely related species of Rubus
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