PMC

Phylogenetic tree inferred by maximum-likelihood (ML) method based on 20 representative species. Prunus domestica and Malus doumeri were used as outgroup taxa. A total of 1000 bootstrap replicates were computed and the bootstrap support values are shown at the branches. The gray lines were used to supplement the branch length, and the branch length of the phylogram was black. The following sequences were used: Rubus glandulosopunctatus MT274118 (Yang et al. ), Rubus rubroangustifolius MT274123 (Yang et al. ), Rubus taiwanicola MT274125 (Yang et al. ), Rubus hirsutus MT663327 (Wang et al. ), Rubus tsangii MT576948, Rubus longisepalus MW436703 (Park et al. ), Rubus chingii OL449946, Rubus chingii MN885523 (Wang et al. ), Rubus takesimensis MG972806 (Yang et al. ), Rubus crataegifolius MG189543 (Yang et al. ), Rubus boninensis MH734123 (Yang et al. ), Rubus trifidus MK465682 (Yang et al. ), Rubus peltatus MT576945 (Yang et al. ), Rubus pinfaensis MZ352081, Rubus columellaris MT576939, Rubus ellipticus MT576935 (Zhu et al. ), Rubus wallichianus MT576941, Rubus ellipticus var. Obcordatus MT576940, Rubus leucanthus MK105853 (Guo et al. ), Rubus xanthocarpus MT576946, Prunus domestica MW406471 (Geng et al. ), and Malus doumeri MN577878 (Wang et al. ).

Chloroplast phylogeny of 38 Rubus species using maximum likelihood (ML) method based on the concatenated LSC, SSC and an IR region. The red fonts represent R. idaeus in this study. Two Rosa species (Rosa sertata and Rosa glomerata) were selected as outgroups. Genbank IDs were listed after the species’ names. Maximum likelihood bootstrap values (BS) are shown at nodes. Branches with no values listed have 100% BS. The following sequences were used: Rubus parvifolius OK127884 (Yu et al. ), Rubus innominatus OK127883 (Yu et al. ), Rubus niveus NC056930, Rubus biflorus NC080344, Rubus phoenicolasius MW115432 (Zhang et al. ), Rubus pileatus NC056947, Rubus irritans NC057600 (Han et al. ), Rubus amabilis NC047211, Rubus sachalinensis NC056965 (Liu et al. ), Rubus idaeus OR698909 (this study), Rubus corchorifolius NC056942, Rubus chingii NC050296 (Wang et al. ), Rubus trianthus NC060616 (Yu et al. ), Rubus hirsutus OK127882 (Yu et al. ), Rubus tsangii NC056940, Rubus rosifolius OL435124 (Yang et al. ), Rubus crataegifolius NC039704 (Yang et al. ), Rubus peltatus NC056937, Rubus xanthocarpus NC056938, Rubus leucanthus MK105853, Rubus columellaris NC056932, Rubus ellipticus NC056929, Rubus wallichianus NC056933, Rubus rufus NC056798, Rubus cochinchinensis NC056289, Rubus pacificus NC064142 (Xiong et al. ), Rubus ichangensis NC056935, Rubus lambertianus OK127886 (Yu et al. ), Rubus buergeri NC072261, Rubus hunanensis OK127885 (Yu et al. ), Rubus tephrodes NC060615 (Yu et al. ), Rubus swinhoei OQ411240, Rubus bambusarum NC056916, Rubus henryi NC056945, Rubus setchuenensis NC056946, Rubus lineatus NC056943, Rubus pentagonus NC056936, Rubus quinquefoliolatus NC063615, Rosa sertata NC066975, Rosa glomerata NC062462 (Chen et al. ).

Rat fed Rubus coreanus byproducts show enhanced galectin-9 development in mesenteric lymph nodes (MLN) and spleen. C, control; T1, 0.5% Rubus coreanus byproducts; T2, 1.0% Rubus coreanus byproducts; T3, 1.5% Rubus coreanus byproducts. The expression of galectin-9 in MLN was higher in the group fed with Rubus coreanus byproducts than in control, and highest in the group of 0.5% Rubus coreanus byproducts. Galectin-9 expression in the spleen was also higher in the group fed with Rubus coreanus byproducts than in control. a-c Means are significantly different within the same row (p<0.05). Data represent means±standard deviation of 6 replicates.

Phylogenetic analysis of the NBS domain was carried out by the neighbor-joining method using RGA sequences of domesticated and wild Malus species (green), Pyrus spp. (yellow), Prunus spp. (purple), Fragaria spp. (red), Rosa spp. (orange), and Rubus spp. (blue). Proteins present in contiguous positions of the tree are merged (collapsed branches are indicated by the + sign). Phylogentec tree indicates 49, three and one clades specific to Malus spp., Fragaria spp. and Rosa spp., respectively. Clades with RGAs of different genera: three clades of Malus spp. and Prunus spp.; seven clades of Malus spp. and Pyrus spp.; two clades of Malus spp. and Rubus spp.; four clades of Malus spp. and Rosa spp.; two clades of Fragaria spp. and Rosa spp.; two clades of Malus spp., Rosa spp., and Rubus spp.; three clades of Malus spp., Pyrus spp., and Rosa spp.; three clades of Malus spp., Prunus spp., and Rubus spp.; four clades of Malus spp., Prunus spp., Rosa spp., and Rubus spp.; three caldes of Malus spp., Prunus spp., Pyrus spp., Rosa spp., and Rubus spp.; two clades of Malus spp., Fragaria spp., Prunus spp., Rosa spp., and Rubus spp., one clade of Malus spp., Fragaria spp., Pyrus spp., Rosa spp., and Rubus spp.