Identification of individual root-knot nematodes using low coverage long-read sequencing

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.

Unstable Phase Response Curves Shown by Spatiotemporal Patterns in the Plant Root Circadian Clock

Phase response curves (PRCs) play important roles in the entrainment of periodic environmental cycles. Measuring the PRC is necessary to elucidate the relationship between environmental cues and the circadian clock. Conversely, the PRCs of plant circadian clocks are unstable due to multiple factors such as biotic/abiotic noise, individual differences, changes in amplitude, growth stage, and organ/tissue specificity. However, evaluating the effect of each factor is important because PRCs are commonly obtained by determining the response of many individuals, which include different amplitude states and organs. The plant root circadian clock spontaneously generates a spatiotemporal pattern called a stripe pattern, whereby all phases of the circadian rhythm exist within an individual root. Therefore, stimulating a plant root expressing this pattern enables phase responses at all phases to be measured using an individual root. In this study, we measured PRCs for thermal stimuli using this spatiotemporal pattern method and found that the PRC changed asymmetrically with positive and negative temperature stimuli. Individual differences were observed for weak but not for strong temperature stimuli. The root PRC changed depending on the amplitude of the circadian rhythm. The PRC in the young root near the hypocotyl was more sensitive than those in older roots or near the tip. Simulation with a phase oscillator model revealed the effect of measurement and internal noises on the PRC. These results indicate that instability in the entrainment of the plant circadian clock involves multiple factors, each having different characteristics. These results may help us understand how plant circadian clocks adapt to unstable environments and how plant circadian clocks with different characteristics, such as organ, age, and amplitude, are integrated within individuals.

Genomic taxonomic assignment of individual root-knot nematodes

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.

Impact of Plant Root Morphology on Rooted-Soil Shear Resistance Using Triaxial Testing

Mechanical reinforcement by plant roots increases the soil shearing strength. The geometric and distribution characteristics of plant roots affect the soil shearing strength. Current research on the shear strength of rooted-soil is mostly based on direct shear tests with a fixed shear surface and thus cannot reflect the actual failure state of the rooted-soil. In this study, Golden Vicary Privet was used to create a rooted-soil, and a triaxial test method was used for soil mechanical property analysis. The influence of the root geometry (root diameter and individual root length) and distribution characteristics (root density and root distribution angle) on the rooted-soil shearing strength was studied by controlling the root morphology in the specimens. According to the results, both the root geometry and distribution characteristics affect the rooted-soil shearing strength. For a fixed total length of the roots, the longer the individual root length is, the better the soil shearing strength is. In addition, the reinforcement effect of the root system increases as the angle between the root and the potential failure surface increases. The results also show that the root system significantly enhances the soil cohesion while only minimally affecting the internal friction angle. The maximum rooted-soil cohesion is 2.39 times that of the plain soil cohesion, and the maximum internal friction angle of rooted-soil is 1.24 times that of plain soil. This paper provides an approach for the determination of the rooted-soil strength and a rationale for vegetation selection in ecological slope reinforcement applications.

Genotypic and Organ Variation in Ginsenoside Contents from American Ginseng Populations

Variation in ginsenoside content was investigated as a function of population/genotype, plant organ, and age using four geographically isolated wild populations and one landrace population of american ginseng (Panax quinquefolius L.). The contents of individual and total ginsenosides were affected by the main and two-way interactions between population, organ, and age. Ginsenoside Re was not detected in roots of the wild population plants but was found in leaves and in both organs of the landrace population. A positive relationship between root age and total root ginsenosides was detected in two wild populations. Individual root ginsenosides were highly correlated with certain leaf ginsenosides in wild populations rather than in landrace populations. Therefore, the results suggest that certain leaf ginsenosides would be applied for potential biomarkers to estimate individual root ginsenosides. Principal component analysis (PCA) scores plot indicates that all wild populations were segregated from the single landrace population. However, cluster analysis indicates that differences existed between organs, and between the wild and landrace populations. Overall, the result suggests that the variation of individual and total ginsenoside contents would be influenced by a combination of population, plant organ, and root age.