To standardize the origin of Rubi Fructus by using ITS2 and matK molecular markers to identify Rubi Fructus and its analogues.

The ITS and matK sequences of Rubus chingii Hu, Rubus corchorifolius L.f., Rubus hirsutus Thunb., Rubus parvifolius L., Rubus buergeri Miq. and Rubus lambertianus Ser. were amplified and sequenced. The hidden Markov model was used to remove 5.8S and 28S from ITS sequences. A total of 25 ITS2 sequences were obtained. And a total of 22 matK sequences were obtained by proofreading by Glustal software. MEGA software was used for matK and ITS2 sequences analysis, intraspecific and interspecific genetic distances caculation, and neighbor joining (NJ) phylogenetic tree construction. ITS2 secondary structure was predicted by ITS2 database and aligned by 4Sale software. Profile neighbor-joining (PNJ) phylogenetic tree was constructed based on combined ITS2 sequence and its secondary structure by ProfDistS software.

An obvious barcoding gap between Rubi Fructus and its analogues was showed. The topological relationship between NJ tree and PNJ tree was consistent, and each taxon exhibits monophyly. The ITS2 secondary structure of Rubi Fructus was significant different from its analogues.

It is recommended that both ITS2 and matK markers can serve as DNA barcodes for identifying Rubi Fructus and its analogues. The addition of ITS2 secondary structure information can enrich the identification results and provide theoretical support for resource research and variety selection of Rubi Fructus.

Rubi Fructus; Molecular identification; ITS2; matK; Screening