Search Results (25)

Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, there is a notable lack of research on its mitogenomes. We utilized PMAT to assemble the mitogenomes of six Rubus species according to long-read HiFi reads and annotated them through homologous alignment. Subsequently, we compared their characteristic differences within Rubus mitogenomes. The complete mitogenomes of R. parviflorus, R. spectabilis, R. idaeus, R. armeniacus, and R. caesius all exhibit master circle structures, with lengths ranging from 360,869 bp to 447,754 bp. However, R. chamaemorus displays a double-circle structure composed of two small circular molecules, spanning 392,134 bp. These mitogenomes encode a total of 54–61 genes, including 33–34 PCGs, 17–24 tRNAs, and 3 rRNA genes. Compared to the other five Rubus species, R. chamaemorus has fewer sequence repeats. These six species exhibit similar codon usage patterns. A large number of gene transfers were detected between organellar genomes of six Rubus species. Additionally, two phylogenetic trees were constructed using 31 mitogenomes and 94 chloroplast genomes, revealing a minor conflict within Rubus. Overall, this study clarifies the mitogenome characteristics of Rubus and provides valuable insights into the evolution of the genus. Full article

Calyptra Ochsenheimer, 1816 is an important genus of fruit piercers and blood feeders with 18 described species worldwide. Both sexes of all Calyptra species pierce fruit. Adults feed upon and damage soft-skinned (e.g., Rubus and Vitis) and thicker-skinned fruits (e.g., Ficus and Citrus) in subtropical and tropical Asia. These moths are rare examples of a lepidopteran lineage that uses its fruit-piercing mouthparts to pierce the skin of vertebrate animals occasionally. In China, 10 species of this genus have been reported. Here, we identified seven species of the genus Calyptra Ochsenheimer, 1816 from Chinese fauna, including C. gruesa, C. thalictri, C. hokkaida, C. albivirgata, C. orthograpta, C. fletcheri, and C. lata. Detailed illustrations of male and female external morphology and genital structures are provided. A comprehensive worldwide checklist of the genus Calyptra is also included. This study highlights significant taxonomic revisions and morphological features for this genus within Chinese fauna. Full article

Food resources are the fundamental basis for the survival and reproduction of animals. Diet research is the foundation for understanding their ecological habits and is of great significance for evaluating their survival status and carrying out effective protection and management. South China sika deer (Cervus nippon kopschi) is the most endangered subspecies of wild sika deer in China, with a small population and a shrinking distribution area. Here, we used DNA metabarcoding technology to study the diet composition of C. n. kopschi in Taohongling Sika Deer National Nature Reserve in Jiangxi, China. Comparative analysis of diet composition among different areas (A–E) of C. n. kopschi was conducted, as well as C. n. hortulorum raised in the same areas. We found that the dominant families in the diet composition of C. n. kopschi were Rosaceae (46.73% of relative abundance), Anacardiaceae (6.02%), Poaceae (5.54%), and Fabaceae (3.92%), with Rubus (45.43%) being the absolute dominant genus. Thirty-two preferred plant species were identified in the diet of C. n. kopschi. The highest relative abundance (45%) was Rubus reflexus. The dominant family and genus in the diet composition of C. n. hortulorum were Fabaceae (33.89%) and Pueraria (32.87%), respectively. Of the 15 preferred plant species, the highest relative abundance was Pueraria montana (33%). The richness, diversity, and evenness of diet composition in Area B of C. n. kopschi were the highest among all areas, with significant differences compared to Areas C, D, and E. Diet composition of deer in Area A did not differ significantly from those in other areas. Principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS) both indicated a significant separation in the diet composition of C. n. kopschi and C. n. hortulorum, while Area B showed significant separation from the other areas. This study elaborates on the diet composition information of C. n. kopschi and can provide a reference for the protection and improvement of the habitat of sika deer. Full article

The aim of this study was to compare the antioxidant potential in the fruits of different hybrids of Rubus idaeus and Rubus occidentalis (four hybrids) against the fruit of known cultivars of both species (R. idaeus—three cultivars; R. occidentalis—five cultivars) and, using chemometric analysis, to select factors affecting the level of polyphenols and antioxidant properties. Antioxidant activity was determined using the ABTS, DPPH and FRAP tests. Chemometric analysis enabled the separation of R. idaeus and R. occidentalis cultivars and classified the hybrid R. idaeus/R. occidentalis R1314701 as belonging to the R. occidentalis species. Moreover, two hybrids, Rubus occidentalis/Rubus idaeus R1613411 and R. idaeus/R. occidentalis R1613409, can be classified as a purple raspberry. Crossbreeding species/cultivars of the Rubus genus may result in an increased content of anthocyanins, but on the other hand, it may lead to a reduction in free radical scavenging activity in the ABTS and DPPH. Spearman’s correlations confirm the correlations between the total polyphenol content and antioxidant activity in the DPPH, ABTS and FRAP, as well as the anthocyanin content and antioxidant activity in the ABTS and FRAP tests. Chemometric analysis can be an effective tool in determining the species affiliation of obtained hybrids and cultivars. Full article

The genus Rubus encompasses over 1000 species, including raspberries and blackberries, known for their rich nutritional and health-promoting properties. This review aims to provide a comprehensive overview of the nutritional values, health benefits, and potential medical and pharmaceutical applications of Rubus species. The fruits, roots, shoots, and leaves of these plants are distinguished by their high content of polyphenols, vitamins, and minerals, which contribute to their potent anti-oxidant, anti-inflammatory, anti-neurodegenerative, and anti-cancer effects. The diverse phytochemical profiles of the Rubus species support their use in the prevention and treatment of chronic diseases such as cardiovascular diseases, diabetes, and certain cancers. Additionally, the Rubus species are valuable as pharmaceutical raw materials due to their bioactive compounds. Despite the focus on a few widely cultivated species, numerous wild and lesser-known Rubus species offer significant untapped potential as functional foods, nutraceuticals, and pharmaceuticals. Future research should explore the detailed mechanisms of their bioactivities, develop effective extraction and formulation techniques, and integrate these findings into public health strategies. The genus Rubus represents a promising resource for enhancing human health and nutrition, as well as for pharmaceutical and medical applications, justifying increased cultivation and utilization of species from this genus. Full article

Rubus includes a group of important plants with medicinal and culinary significance, as well as ornamental value. However, due to its status as one of the largest genera in the Rosaceae family and frequent occurrences of apomixis, hybridization, and polyploidy among its species, the morphological identification of this genus is highly challenging. The plastid genome serves as a valuable tool for studying the evolutionary relationships among plants. Therefore, based on the raw data of the whole genomes from six popular Rubus taxa, the complete Cp genomes were assembled, annotated, and subjected to comparative and phylogenetic analyses. In this research, six newly complete Cp genomes were reported, which all had a representative quadripartite formation, with a similar GC content (37.06%–37.26%), and their size ranged from 155,493 bp to 156,882 bp. They all encode 111 unique genes, containing 79 PCGs, 28 tRNA, and 4 rRNA. The analysis of gene structure of different groups showed that the sequence and content of genes were relatively conservative, and there was no gene rearrangement. Most of their PCGs had a high frequency codon usage bias and all genes were in purifying selection states. A nucleotide variable analysis revealed that the IR areas had less variation than the SC areas, and there was the greatest diversity in the SSC area. Eleven hypervariable areas were identified, containing rpl32-trnL, rpl32, rps16-trnQ, trnT-trnL, trnQ-psbK, trnK-rps16, and rps15-ycf1, which could be used as labels for genetic diversity and taxa identification. The phylogenetic trees of 72 Rosaceae plants were constructed based on ML and BI methods. The results strongly support the theory that the Rubus genus was a monophyletic group and sampled species could be arranged into seven subgenera. Overall, this study sheds its new light into the phylogeny of the Rubus genus, providing valuable insights for future studies of the Cp genomes from the expanded taxa of the Rosaceae family. Full article

With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus. Full article

Helicobacter pylori infections are still an important health problem and are directly related to the development of gastric ulcer, gastric adenocarcinoma, mucosal lymphoid tissue lymphoma, and diabetes. At the same time, the number of substances/drugs effective against these bacteria is limited due to increasing resistance. Raw plant materials from various species of the Rubus genus—fruits and shoots—have shown antimicrobial activity in numerous studies against different bacteria, including H. pylori in a planktonic form. Research carried out on a model using fragments of intravenous infusions and triphenyl tetrazolium chloride (TTC) as a dye showed that the shoot extract of Rubus idaeus ‘Willamette’, the fruit extract of R. idaeus ‘Poranna Rosa’, R. idaeus and R. idaeus ‘Laszka’, and R. occidentalis Litacz’ prevent the formation of biofilm by H. pylori. Active concentrations inhibiting biofilm formation were 6.65 mg/mL for shoots and 16.65 mg/mL for fruits. However, in the resulting biofilm, the extract from the shoots of R. idaeus ‘Willamette’ and the fruit of R. idaeus ‘Poranna Rosa’ at a concentration of 16.65 mg/mL was active against living bacteria, and the remaining extracts showed such activity at a concentration of 33.3 mg/mL. In studies on the interaction of the extract with antibiotics on biofilm, the extract from the shoots of R. idaeus ‘Willamette’ showed synergy with doxycycline and levofloxacin, additivity with amoxicillin and clarithromycin, and neutrality with metronidazole. H. pylori biofilm research was carried out in a newly elaborated research model—culture on fragments of intravenous infusions with the addition of TTC as a marker of living bacterial cells. The research results may constitute the basis for the development of new combination therapies for the treatment of H. pylori infections, including its resistant strains. The proposed new biofilm research model, which is cheap and effective, may allow testing of new substances that are potentially more effective against H. pylori and other biofilm-forming bacterial strains. Full article

Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies. Full article

A cane disease of a non-commercial thornless blackberry cultivar (genus Rubus, subgenus Rubus Watson) obtained in a breeding program was observed in May 2021 in northern Spain during a field evaluation. Symptoms of the disease appeared in spring and firstly consisted of dark-brown lesions in the petioles, tips, and intermediate zones of the canes, finally causing the leaves, canes, and lateral shoots to die. Two strains were recovered from infected canes and identified by morphological characteristics and multigene analysis as Gnomoniopsis idaeicola (LPPAF-977) and Diaporthe rudis (LPPAF-981). Pathogenicity tests showed that both fungi caused shoot dieback when artificially inoculated, reproducing the symptoms originally observed. Moreover, tissue necrosis was enhanced when Diaporthe rudis and Gnomoniopsis idaeicola were co-inoculated. This is the first report of Diaporthe rudis and Gnomoniopsis idaeicola causing a potentially serious disease to blackberries in Spain. Full article

Tympanis species (Leotiales) are plant pathogens distributed mostly in northern temperate ecosystems. The diversity and identity of some species remains unclear. Tympanis vagabunda, found in Sicilia (Italy) on dry twigs of Rosa, Rubus, and Pistacia, is one example of an obscure and poorly known species. During the study of its type specimen in S, which contained one twig with a wood anatomy fitting neither of the three mentioned hosts, the microanatomic structures indicated that it belongs to the genus Rutstroemia (Helotiales). To investigate its identity, the types of R. fruticeti, R. juniperi, R. urceolus, and R. longiasca were studied for comparison. The species for which molecular data were available were included in a dataset that contained identified species of Rutstroemia, along with other select species from the families Rutstroemiaceae and Sclerotiniaceae. R. fruticeti, a saprobe frequently reported from Rubus fruticosus in Europe, is found to be a later synonym of T. vagabunda, and the combination Rutstroemia vagabunda is proposed. R. juniperi is an infrequently reported European species on twigs of Juniperus and is morphologically hard to distinguish from R. vagabunda; available molecular data support its recognition as a distinct species. R. longiasca differs from R. vagabunda in its black apothecia, smaller asci, and narrower ascospores. R. urceolus differs from R. vagabunda in having black apothecia and smaller inamyloid asci, and excipulum at the flanks and margin is composed of dark-walled hyphae. Full article

This study examines culturable diazotrophs and non-culturable bacteria found in the rhizospheres and root pseudonodules of wild blackberry plants (Rubus ulmifolius) that dwell on an unmanaged calcareous nitrogen-deficient soil. The DNA was extracted from the nodules and rhizospheres, and 16S rRNA gene metabarcoding was carried out. The metagenome functions were predicted with bioinformatic approaches. The soil samples were analyzed for the physico-chemical properties. The culturable diazotrophs were isolated and evaluated for the biochemical and plant growth-promoting properties. The soil was classified as nutrient-depleted calcareous soil. The microbial communities of the nodules and rhizospheres showed marked differences. The Pseudomonadota was the nodules’ dominant phyla (90%), while the Actinobacteriota was the most abundant (63%) in the rhizospheres. Stenotrophomonas was the dominant genus (55%) in the nodules, while the Streptomyces genus was widely present (39%) in the rhizospheres. The differences among the nodule and rhizosphere microbial communities were also highlighted by the metagenome function predictions. The gene copies (KOs) revealed the most interesting findings. Similar KOs involved in the nitrogen fixation were found to be similar in terms of the nodules and rhizospheres. However, the nitrate reduction was higher in the rhizosphere, while the denitrification was more prominent in the nodules. Nine diazotrophs were isolated from the nodules and rhizospheres. The plant growth promoting traits’ characterization has shown the interesting potential of the isolates in improving the acquisition of nutrients in plants, promoting their growth, and tolerating stress. Based on interesting biochemical and plant growth-promoting traits, the isolate N2A was further characterized and identified as Pantoea agglomerans. Full article

Pollen morphology is one of the important vehicles in resolving some taxonomic problems on the family, genera or species level and has become part of the many disciplines and collaborative approaches in plant systematics and evolution. Palynological studies on the large and taxonomically highly complex genus Rubus L. have been limited, particularly concerning pollen variability. The aim of current study was to investigate the scope of inter- and intraspecific variability of the studied species based on pollen morphology, as well as verify taxonomic usefulness of pollen traits in distinguishing the studied taxa. The sixteen native Poland and Europe Rubus species were studied. Over a dozen quantitative and qualitative features of 2100 pollen (70 samples of 30 pollen each) were analyzed. Exine ornamentation and pollen size proved to be most useful pollen traits in the assessment of variability in the studied Rubus species. Pollen traits did not confirm the currently adopted taxonomical division of the genus Rubus into subgenera, sections and series. The greatest interspecific variability was found for traits P, E, Le and d, while variability was lowest in the case of Exp, Exe, P/E, Le/P, d/E, Exp/P and Exe/E. Intraspecific variability was determined by the following features ordered from those least to most variable: P, E, d, Le, d/E, Exp/P, Exp, P/E and Le/P. Full article

The plants of the genus Rubus (R.) are applied as antiseptic agents in the treatment of skin diseases. Despite the great interest in plants of this genus, there are few reports on the antioxidant and biological activities of preparations obtained from the leaves of these plants. Therefore, we decided to evaluate the antioxidant activity of preparations from leaves of wild plant species of the genus Rubus using the frequently applied DPPH, ABTS, and FRAP methods, as well as to determine the total polyphenol content using the Folin–Ciocalteau method and perform qualitative evaluation by gas chromatography–mass spectrometry (GC-MS). The bactericidal and fungicidal activities of the obtained preparations were evaluated by applying laboratory tests: using the disc and the well methods based on the standards EN 13697:2019, EN 13697:2015, and EN 1500:2013. Microbiological tests of the plant preparations against bacteria, fungi, and yeasts isolated from the environment and against reference strains were performed. Moreover, antimicrobial testing of antibiotics against the tested strains was performed for comparison. The n-octanol/water partition coefficient of the obtained preparations was determined by the shake-flask method to determine their lipophilicity. According to the results, a high content of polyphenols and other antioxidant and biologically active compounds can be thought of as the parameter responsible for the effective activity of plant preparations obtained from wild plant species of the genus Rubus. The methods for determining bactericidal and fungicidal activity clearly demonstrates that preparations with reduced ethanol content exhibit bactericidal and fungicidal activity on surfaces. Testing of hand disinfection by means of rubbing with the preparations confirmed their antimicrobial activity against Escherichia coli K12 NCTC 10538. The obtained results show that the tested preparations exhibit on average two times lower activity against the reference bacterial strains than comparable antibiotics. The preparations obtained from the leaves of R. idaeus L. and R. fruticosus L. could complement classical antibiotics. While environmental bacteria showed a similar response to the preparations and antibiotics, their sensitivity was about one-third less than that of the reference strains. Our studies have shown that the obtained preparations are highly hydrophilic (logP < 0). Thus, these preparations can only be used in lipid bilayers in the aqueous core of liposomes, not in the lipid envelope. Full article

Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural “supergenus” for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies. Full article