AUTHOR=Wang Yan , Chen Qing , Chen Tao , Tang Haoru , Liu Lin , Wang Xiaorong 

TITLE=Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.00968

DOI=10.3389/fpls.2016.00968

ISSN=1664-462X

ABSTRACT=<p><italic>Rubus</italic> L. is a large and taxonomically complex genus, species of which exhibit apomixis, polyploidy, and frequent hybridization. Most of Chinese <italic>Rubus</italic> are assigned in two major sections, <italic>Idaeobatus</italic> and <italic>Malachobatus</italic>. To explore the phylogenetic relationships within Chinese <italic>Rubus</italic>, inferences upon three chloroplast DNA (<italic>rbc</italic>L, <italic>rpl</italic>20-<italic>rps</italic>12, and <italic>trn</italic>G-<italic>trn</italic>S), nuclear ribosomal ITS, and two low-copy nuclear markers (<italic>GBSS</italic>I-2 and <italic>PEPC</italic>) were deduced in 142 <italic>Rubus</italic> taxa from 17 subsections in 6 sections. <italic>nrITS</italic> and <italic>GBSS</italic>I-2 were the most informative among the six DNA regions assessed. Phylogenetic relationships within <italic>Rubus</italic> were well-resolved by combined nuclear datasets rather than chloroplast markers. The phylogenetic inferences strongly supported that section <italic>Idaeobatus</italic> was a polyphyletic group with four distant clades. All samples of sect. <italic>Malachobatus</italic> formed a monophyletic clade, in which <italic>R. tsangorum</italic> and <italic>R. amphidasys</italic> of sect. <italic>Dalibardastrum</italic>, and <italic>R. peltatus</italic> from subsection <italic>Peltati</italic> of sect. <italic>Idaeobatus</italic> were always nested. <italic>Rubus pentagonus</italic> (2<italic>n</italic> = 2<italic>x</italic> = 14) from subsect. <italic>Alpestres</italic> of sect. <italic>Idaeobatus</italic> was a sister group to the polyploid sect. <italic>Malachobatus</italic>, as well as the polytomy of three sect. <italic>Cyalctis</italic> members. This suggests that some polyploids of <italic>Malachobatus</italic> might originate from common ancestors, via polyploidization of hybrids between <italic>R. pentagonus</italic> and sect. <italic>Cylactis</italic> species. They had experienced species explosion in a short time. Section <italic>Dalibardastrum</italic> species have potential parental lineages from subsects. <italic>Moluccani</italic> and <italic>Stipulosi</italic> of sect. <italic>Malachobatus</italic>. Based on molecular phylogenies, we also provided recommendations for the taxonomic treatments of four taxa. In addition, our results showed certain incongruence between chloroplast and nuclear markers, which might be due to hybridization and introgression.</p>