Phylogeny of Chinese Rubus (Rosaceae) based on nuclear ribosomal internal transcribed spacer (ITS) sequences

Yan Wang, Qing Chen, Haoru Tang, Xiaorong Wang
The genus Rubus Linnaeus belongs to the subfamily Rosoideae, and the family Rosaceae. It is a large and taxonomically complex genus, species of which exhibits agamospermy, polyploidy, and frequent hybridization. Southwestern China is proposed to be a major center of origination for Rubus, because of the rich morphological diversity, large number of subgenera, and extensive variations there. Chinese Rubus is composed of 24 subsections in 8 sections, and most species are assigned in two major sections, Idaeobatus and Malachobatus. In this study, we collected 105 Rubus taxa from 17 subsections in 6 sections, Idaeobatus, Rubus, Malachobatus, Dalibardastrum, Chamaebatus, and Cylactis, as well as two outgroups, Fragaria vesca L. and Rosa banksiae Ait. Our goal is to elucidate the phylogenetic relationships among Chinese Rubus and understand the evolutionary history involved in the species in Rubus based on nuclear ribosomal internal transcribed spacer (nrITS). The ITS alignment of Rubus includes 264 bp of ITS1, 164 bp of 5.8S rDNA, 212 bp of ITS2. Together with outgroups, the final ITS dataset contains 107 accessions and 645 aligned nucleotides, of which 201 (31.16%) are variable and 122 (18.91%) are parsimony informative. Specifically, this region evolves three times within species of sect. Idaeobatus than that of sect. Malachobatus. Phylogenetic analysis of the ITS dataset indicates the following results. The genus Rubus forms a strongly supported monophyletic group, while section Idaeobatus is recovered as polyphyly split into four distant lineages. All samples of sect. Malachobatus cluster together to form a monophyletic clade, in which R. tsangorum and R. amphidasys of sect. Dalibardastrum, as well as R. peltatus from subsection Peltati of sect. Idaeobatus are nested. Rubus pentagonus (2n=2x=14) from subsect. Alpestres of sect. Idaeobatus is sister to Malachobatus, a section which are exclusively polyploid. The result suggests that the polyploids might have common ancient diploid ancestors with R. pentagonus. In addition, species of sect. Dalibardastrum probably have potential parental lineages from sect. Malachobatus. Three sect. Cylactis members, R. fockeanus, R. nyalamensis, and R. fragarioides var. pubescens, occur at largely divergent phylogenetic positions, strongly indicating its polyphyly. ITS region is demonstrated to be extremely useful for reconstructing phylogeny of Chinese Rubus species.
Wang, Yan, Chen, Qing, Tang, Haoru and Wang, Xiaorong (2018). Phylogeny of Chinese Rubus (Rosaceae) based on nuclear ribosomal internal transcribed spacer (ITS) sequences. Acta Hortic. 1208, 13-24
DOI: 10.17660/ActaHortic.2018.1208.3
Chinese Rubus, ITS, phylogeny, section Idaeobatus, section Malachobatus

Acta Horticulturae