Japanese knotweed (Fallopia japonica): an analysis of capacity to cause structural damage (compared to other plants) and typical rhizome extension

The mixed auto-/allooctoploid genome of Japanese knotweed (Reynoutria japonica) provides insights into its polyploid origin and invasiveness

Reynoutria japonica Houtt. (Polygonaceae), a traditional Chinese medicine, is one of the top 100 most destructive invasive species worldwide due to its aggressive growth and strong adaptability. Here, we report an 8.04 Gb chromosome-scale assembly of R. japonica with 88 chromosomes across eight homologous sets. Through a combined phylogenetic and genomic analysis, we demonstrate that R. japonica is a mixed auto-/allooctoploid (AAAABBBB). Subgenome A (SubA) exhibited a close phylogenetic relationship with the related species Fallopia multiflora. We also unveiled the origin and evolutionary history of octoploid R. japonica based on resequencing data from Reynoutria species with different ploidy. Comparative genomics analysis revealed the genetic basis of R. japonica's invasivity and adaptability. The auxin response factor (ARF) gene family was significantly expanded in R. japonica, and these genes were highly expressed in rhizomes. We also investigated the collaboration and differentiation of the duplicated genes resulting from auto- and allo-polyploidization at the genomic variation, gene family evolution, and gene expression levels in R. japonica. Transcriptomic analysis of stem internodes and apices at different developmental stages revealed that the octuplication and significant expansion of the SAUR19 and SAUR63 subfamilies due to tandem replication in SubA, and the high expression of these genes in stems, likely contribute to the rapid growth of R. japonica. Our study provides important clues into adaptive evolution and polyploidy dominant traits in invasive plants, and will also provide important guidance for the breeding of polyploid crops.

Attenuated total reflection Fourier-transform infrared spectroscopy for the prediction of hormone concentrations in plants

Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed (Reynoutria japonica) plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches.

Evaluation of the Main Macro-, Micro- and Trace Elements Found in Fallopia japonica Plants and Their Traceability in Its Honey: A Case Study from the Northwestern and Western Part of Romania

Fallopia japonica (Japanese knotweed, Reynoutria japonica or Polygonum cuspidatum) is considered an extremely invasive plant worldwide and a bioindicator of heavy metals. Yet, its potential as a crop for honeybees is still underevaluated. This study employs atomic absorption spectrometry to quantitatively analyze the concentration of macro-elements, namely, calcium (Ca), potassium (K) and magnesium (Mg); micro-elements, such as copper (Cu), iron (Fe), manganese (Mn) and selenium (Se); and trace elements, i.e., cadmium (Cd), chromium (Cr), nickel (Ni) and lead (Pb) in different anatomic parts of Fallopia japonica (FJ) plants (roots, rhizomes, stems, leaves) and their traceability into honey. This research encompasses a thorough examination of samples collected from the northwestern and western part of Romania, providing insights into their elemental composition. The results showed that the level of trace elements decreases in terms of traceability in honey samples (Pb was not detected in any of the analyzed samples, while Cd had a minimum content 0.001 mg/kg), ensuring its quality and health safety for consumption. Moreover, the data generated can function as a valuable resource to explore the plant's positive eco-friendly impacts, particularly in relation to its honey.

A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different Reynoutria japonica Populations

Reynoutria japonica Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role in population diversity analysis. However, there are few studies on the chloroplast genome of R. japonica. In this study, the complete chloroplast genomes of three R. japonica from different regions were performed by next-generation sequencing technology. The results revealed that the lengths of the three chloroplast genomes are between 163,371~163,372 bp, and they have a highly conserved structure with a pair of inverted repeat (IR) regions (31,121 bp), a large single-copy (LSC) region (87,571~87,572 bp), and a small single-copy (SSC) region (13,558 bp). In total, 132 genes were annotated, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. The phylogenetic analysis strongly revealed that 13 populations of R. japonica form a monophyly, and Fallopia multiflora (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and R. japonica in China could be further divided into two major groups based on genetic structure analysis. In addition, several potential loci with suitable polymorphism were identified as molecular markers. Our study provides important genetic resources for further development and utilization of R. japonica germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.

Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control

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.

Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy

BACKGROUND

Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed.

RESULTS

We have shown distinct differences in the spectral fingerprint region (1800-900 cm^- 1) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics.

CONCLUSIONS

These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats.

Review of Existing Knowledge and Practices of Tarping for the Control of Invasive Knotweeds

Managing invasive exotic plant species is a complex challenge, especially for Asian knotweeds (Reynoutria spp.). Tarping is a regularly cited but poorly documented control method, which consists of covering the ground with a tarp (agricultural tarp, geotextile, geomembrane, etc.) to create a physical barrier to hinder plant growth and deprive the plants of light in order to deplete their rhizomatous reserves. To improve our knowledge of tarping in order to identify the key factors of its success or failure, we reviewed the relevant grey and scientific literature and conducted an international survey among managers to collect feedback on tarping experiments. In the literature, as well as in the field, practices are quite heterogeneous, and the method’s effectiveness is highly contrasted. A better consideration of knotweed biology may improve the efficacy of the method. Based on the bibliography and survey work, we propose practical recommendations including covering the entire stand, extending the tarping up to 2.5 m beyond its edges for a period of at least six years, and ensuring regular monitoring. Even though tarping does not seem to be a one-size-fits-all solution to eradicate knotweed, it could still be a useful control method once knotweed has become a critical management issue.

Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy

Reynoutria japonica (Japanese knotweed) is a problematic invasive plant found in many areas of Europe and North America. Notably, in the UK, the species can cause issues with mortgage acquisition. Control of R. japonica is complicated by its ability to regenerate from small fragments of plant material; however, there remains uncertainty about how much (in terms of mass) rhizome is required for successful regeneration. This study investigated the ability of crowns and rhizomes with different numbers of nodes to regenerate successfully from three sites in the north of England, UK. Two of the sites had been subject to herbicide treatment for two years prior to sampling and the third site had no history of herbicide treatment. No significant differences were observed in regenerated stem diameter, maximum height of stem and maximum growth increments among crowns. All traits measured from the planted crowns were significantly greater than those of the planted rhizome fragments and at least one node was necessary for successful regeneration of rhizomes. The smallest initial fragment weight to regenerate and survive the experiment was 0.5 g. Subjecting all plant material to desiccation for 38 days resulted in no regrowth (emergence or regeneration) after replanting. These findings suggest that desiccation could be a valuable management strategy for small to medium scale infestations common in urban settings.

A benefit-cost analysis framework for prioritization of control programs for well-established invasive alien species

Invasive alien species (IAS) are identified as a major threat to biodiversity and ecosystem services. While early detection and control programs to avoid establishments of new alien species can be very cost-effective, control costs for well-established species can be enormous. Many of these well-established species constitute severe or high ecological impact and are thus likely to be included in control programs. However, due to limited funds, we need to prioritize which species to control according to the gains in ecological status and human well-being compared to the costs. Benefit-Cost Analysis (BCA) provides such a tool but has been hampered by the difficulties in assessing the overall social benefits on the same monetary scale as the control costs. In order to overcome this obstacle, we combine a non-monetary benefit assessment tool with the ecosystem service framework to create a benefit assessment in line with the welfare economic underpinnings of BCA. Our simplified BCA prioritization tool enables us to conduct rapid and cheap appraisals of large numbers of invasive species that the Norwegian Biodiversity Information Centre has found to cause negative ecological impacts. We demonstrate this application on 30 well-established invasive alien vascular plant species in Norway. Social benefits are calculated and aggregated on a benefit point scale for six impact categories: four types of ecosystem services (supporting, provisioning, regulating and cultural), human health and infrastructure impacts. Total benefit points are then compared to the total control costs of programs aiming at eradicating individual IAS across Norway or in selected vulnerable ecosystems. Although there are uncertainties with regards to IAS population size, benefits assessment and control program effectiveness and costs; our simplified BCA tool identified six species associated with robust low cost-benefit ratios in terms of control costs (in million USD) per benefit point. As a large share of public funds for eradication of IAS is currently spent on control programs for other plant species, we recommend that the environmental authorities at all levels use our BCA prioritization tool to increase the social benefits of their limited IAS control budgets. In order to maximize the net social benefits of IAS control programs, environmental valuation studies of their ecosystem service benefits are needed.

Please don’t mow the Japanese knotweed!

Letter To The Editor