Explore the vast range of titles available.

Background Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. Results The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes ( rbcL  +  matK  + nrITS, 56%). Five newly screened gene regions ( ndhF , trnS-G , trnC-petN , ndhF-rpl32 , rpl32-trnL ) had high species resolution, where ndhF and trnS - G were able to distinguish the highest proportion of Calligonum species (56%). Conclusions The entire plastid genome was the most effective barcode for the genus Calligonum , although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum .

Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems.

Extreme weather and globalisation leave our climate vulnerable to invasion by alien species, which have negative impacts on the economy, biodiversity, and ecosystem services. Rapid and accurate identification is key to the control of invasive alien species. However, visually similar species hinder conservation efforts, for example hybrids within the Japanese Knotweed complex. We applied the novel method of ATR-FTIR spectroscopy combined with chemometrics (mathematics applied to chemical data) to historic herbarium samples, taking 1580 spectra in total. Samples included five species from within the interbreeding Japanese Knotweed complex (including three varieties of Japanese Knotweed), six hybrids and five species from the wider Polygonaceae family. Spectral data from herbarium specimens were analysed with several chemometric techniques: support vector machines (SVM) for differentiation between plant types, supported by ploidy levels; principal component analysis loadings and spectral biomarkers to explore differences between the highly invasive Reynoutria japonica var. japonica and its non-invasive counterpart Reynoutria japonica var. compacta ; hierarchical cluster analysis (HCA) to investigate the relationship between plants within the Polygonaceae family, of the Fallopia , Reynoutria , Rumex and Fagopyrum genera. ATR-FTIR spectroscopy coupled with SVM successfully differentiated between plant type, leaf surface and geographical location, even in herbarium samples of varying age. Differences between Reynoutria japonica var. japonica and Reynoutria japonica var. compacta included the presence of two polysaccharides, glucomannan and xyloglucan, at higher concentrations in Reynoutria japonica var. japonica than Reynoutria japonica var. compacta . HCA analysis indicated that potential genetic linkages are sometimes masked by environmental factors; an effect that can either be reduced or encouraged by altering the input parameters. Entering the absorbance values for key wavenumbers, previously highlighted by principal component analysis loadings, favours linkages in the resultant HCA dendrogram corresponding to expected genetic relationships, whilst environmental associations are encouraged using the spectral fingerprint region. The ability to distinguish between closely related interbreeding species and hybrids, based on their spectral signature, raises the possibility of using this approach for determining the origin of Japanese knotweed infestations in legal cases where the clonal nature of plants currently makes this difficult and for the targeted control of species and hybrids. These techniques also provide a new method for supporting biogeographical studies.

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes.

The three highly invasive Reynoutria species – R. japonica Houtt., Reynoutria sachalinensis (F.Schmidt) Nakai, and a hybrid of them – R. x bohemica J. Chrtek & A. Chrtková are rich sources of biologically active compounds. However, only R. japonica is accepted as an herbal drug source in the pharmacopeias as Polygoni cuspidati rhizoma et radix , while R. sachalinensis is used in folk phytotherapy. The hybrid species can be misidentified as R. japonica due to its morphological resemblance. This study intended to explore genetic identity, diversity, and population structure using sequence-related amplified polymorphisms (SRAP) and start codon targeted (SCoT) markers correlated with morphological characteristics and metabolic profiles in fifteen accessions of Reynoutria species from invasive populations in Central Europe (Wroclaw, south-west Poland). The results suggest that morphological identification based on leaf morphology is clear for R. sachalinensis but fails to distinguish between R. japonica and R . × bohemica unambiguously. The qualitative HPLC/DAD/ESI-HR-QTOF-MS analysis determined the chemical composition of collected samples, revealing 117 compounds belonging to carbohydrates, stilbenes, flavan-3-ols, procyanidins, anthraquinones, organic acids, and naphthalenes. Out of these, the six compounds were quantitated. Based on LC-MS data for 117 compounds, the cluster analysis categorized the fifteen accessions into two distinctive clusters. All SCoT and SRAP markers showed medium (0.1 to 0.25) to high (0.30 to 0.40) levels of PIC, high levels of polymorphic bands (85 and 89%, respectively) and relatively high mean values for Rp (6.42 and 7.0) and were considered informative and differentiating. Partitioning the genetic diversity with AMOVA showed that variation within the populations was higher than among them, as seen in the combined data from SCoT and SRAP (53.04% vs. 46.96%, respectively) and the analyses of individual markers. Genetic diversity indices revealed that chosen genetic markers efficiently assess the variability within the genus Reynoutria . Na varied from 1.57 in R. sachalinensis to 3.34 in R. x bohemica , and Ne was low and almost identical for all species (~ 1.6). Nei’s diversity (H) indicated low genetic diversity (< 0.2) in all species, with the highest value for hybrid (0.184). Despite low H values, Shannon’s index (I) remains high and similar ( R. japonica − 5.21, R. x bohemica – 5.28, and R. sachalinensis − 5.45). The number (NPL) and percentage of polymorphic loci (PPL) for the hybrid (160 and 52.98%) were almost twice as high as for the parent species. The populations exhibited moderate G ST values (0.159) and a gene flow (Nm = 1.317). Genetic structure analysis with the Evanno test (ΔK = 2) reveals two genetic groups with the highest admixture in the hybrid population. The cluster analysis dendrograms based on LC-MS data, genetic distance, and leaf morphology categorized the fifteen accessions into three clusters, revealing unequivocal separation of the R. sachalinensis from both other taxa. According to Baker’s methodology, the highest correlation between dendrograms was observed between genetic and morphological data, with values of 0.85. Lower correlations were noted between molecular markers and phytochemical profile, as well as between morphology and phytochemical profile. The study suggests the effectiveness of combined morphological, phytochemical, and SCoT and SRAP molecular marker systems in assessing the identity of plant material. This approach can also be used in further studies on the population structure, spread, diversity, and evolution of invasive species such as Reynoutria spp.

Background The Polygonaceae is a family well-known for its weeds, and edible plants, Fagopyrum (buckwheat) and Rheum (rhubarb), which are primarily herbaceous and temperate in distribution. Yet, the family also contains a number of lineages that are principally distributed in the tropics and subtropics. Notably, these lineages are woody, unlike their temperate relatives. To date, full-genome sequencing has focused on the temperate and herbaceous taxa. In an effort to increase breadth of genetic knowledge of the Polygonaceae, we here present six fully assembled and annotated chloroplast genomes from six of the tropical, woody genera: Coccoloba rugosa (a narrow and endangered Puerto Rican endemic), Gymnopodium floribundum , Neomillspaughia emarginata , Podopterus mexicanus , Ruprechtia coriacea , and Triplaris cumingiana . Results These assemblies represent the first publicly-available assembled and annotated plastomes for the genera Podopterus , Gymnopodium , and Neomillspaughia , and the first assembled and annotated plastomes for the species Coccoloba rugosa , Ruprechtia coriacea , and Triplaris cumingiana . We found the assembled chloroplast genomes to be above the median size of Polygonaceae plastomes, but otherwise exhibit features typical of the family. The features of greatest sequence variation are found among the ndh genes and in the small single copy (SSC) region of the plastome. The inverted repeats show high GC content and little sequence variation across genera. When placed in a phylogenetic context, our sequences were resolved within the Eriogonoideae. Conclusions These six plastomes from among the tropical woody Polygonaceae appear typical within the family. The plastome assembly of Ruprechtia coriacea presented here calls into question the sequence identity of a previously published plastome assembly of R. albida .

Key message Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86–77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.

The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum . All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1 , mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc , atp8 and nad4 , showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii . Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum , indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum , projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum . This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.

Background Persicaria amphibia , a member of the Polygonaceae family, exists both aquatic and terrestrial forms. It is native to North America, Asia, Europe, and some parts of Africa. Objective This study aimed to determine the genetic diversity within and among populations of P. amphibia and the distribution characteristics of each population to investigate insights into the genetic structure and conservation of P. amphibia . Methods In this study, the genetic diversity and structure of 84 P. amphibia individuals from 7 populations in South Korea were analyzed using genotyping-by-sequencing (GBS). We used 2,469 single nucleotide polymorphisms (SNPs) to analyze genetic diversity, principal components, structure, and phylogeny. Results Our results showed a mean observed heterozygosity and mean expected heterozygosity of 0.34409 and 0.34082, respectively. Genetic diversity analysis indicated that the variation among populations (60.08%) was greater than that within populations (39.92%). Fixation index values, principal components analysis, structure, and phylogeny analyses showed that the population in Gyodongdo, Ganghwa Island was highly different. Conclusion These results provide important insights for better understand the population history and genetic structure of P. amphibia .

Bistorta vivipara is a medicinal plant with a long history, but there are few studies on the effects of its medicinal components and endophytic bacteria on the accumulation of secondary metabolites. Therefore, in this study, non-targeted metabolomics techniques and 16s rDNA techniques were used to study B. vivipara from different regions. A total of 1290 metabolites and 437 differential metabolites were identified from all samples. Among them, flavonoids, isoflavonoids, and benzopyrans are the main medicinal components of B. vivipara; these have potential anticancer, antiviral, and antioxidant properties, as well as potential applications for the treatment of atrial fibrillation. In addition, irigenin, an important medicinal component, was identified for the first time. The endophytic bacterial communities in the root tissues of B. vivipara from different regions were also different in composition and richness. Hierarchical clustering heat map analysis showed that Proteobacteria and Actinobacteriota bacteria significantly affected the accumulation of many medicinal components in the roots of B. vivipara.