Protocol for Cas9-targeted long-read sequencing in Globodera pallida and Globodera rostochiensis.

We present a protocol to achieve a higher depth of long-read sequencing of region(s) of interest in potato cyst nematodes without amplification using a Cas9-based Nanopore enrichment approach. We describe steps for designing high-fidelity guide RNAs to be used with Cas9 nuclease, extracting high-molecular-weight DNA from the nematodes, and dephosphorylating genomic DNA ends. We then detail procedures for using Cas9-guide RNA complex to make targeted cleavage of the region of interest followed by a Nanopore library preparation.

A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes.

Pathogens are engaged in a fierce evolutionary arms race with their host. The genes at the forefront of the engagement between kingdoms are often part of diverse and highly mutable gene families. Even in this context, we discovered unprecedented variation in the hyper-variable (HYP) effectors of plant-parasitic nematodes.

A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes.

Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.

Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes.

Background: Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant.

Phosphate Recovery from Urine-Equivalent Solutions for Fertilizer Production for Plant Growth.

This study presents a proof of concept for the recovery of phosphate from aqueous solutions with high phosphorus (PO-P) initial contents to simulate the concentration of streams from decentralized wastewater systems. Solutions with ∼500 ppm phosphorus enable phosphate adsorption and recovery, in contrast to the highly diluted inlet streams (<10 ppm) from centralized wastewater treatment plants. In this work, Mg-Fe layered double hydroxide is used as a phosphate adsorbent, demonstrating its separation from aqueous streams, recovery, and use as a fertilizer following the principles of circular economy.

Unlocking the development- and physiology-altering 'effector toolbox' of plant-parasitic nematodes.

Plant parasites take advantage of host developmental plasticity to elicit profound developmental and physiological changes. In the case of plant-parasitic nematodes (PPNs), these changes can result in the development of new plant organs. Despite the importance of the development- and physiology-altering abilities of these parasites in pathology, research has historically focused on their abilities to suppress immunity.

Integrated Nematode Management in a World in Transition: Constraints, Policy, Processes, and Technologies for the Future.

Plant-parasitic nematodes are one of the most insidious pests limiting agricultural production, parasitizing mostly belowground and occasionally aboveground plant parts. They are an important and underestimated component of the estimated 30% yield loss inflicted on crops globally by biotic constraints. Nematode damage is intensified by interactions with biotic and abiotic factors constraints: soilborne pathogens, soil fertility degradation, reduced soil biodiversity, climate variability, and policies influencing the development of improved management options.

A low-cost and open-source solution to automate imaging and analysis of cyst nematode infection assays for Arabidopsis thaliana.

Background: Cyst nematodes are one of the major groups of plant-parasitic nematode, responsible for considerable crop losses worldwide. Improving genetic resources, and therefore resistant cultivars, is an ongoing focus of many pest management strategies. One of the major bottlenecks in identifying the plant genes that impact the infection, and thus the yield, is phenotyping.

The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.

Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages.

The DNA methylation landscape of the root-knot nematode-induced pseudo-organ, the gall, in Arabidopsis, is dynamic, contrasting over time, and critically important for successful parasitism.

Root-knot nematodes (RKNs) induce giant cells (GCs) within galls which are characterized by large-scale gene repression at early stages. However, the epigenetic mechanism(s) underlying gene silencing is (are) still poorly characterized. DNA methylation in Arabidopsis galls induced by Meloidogyne javanica was studied at crucial infection stages (3 d post-infection (dpi) and 14 dpi) using enzymatic, cytological, and sequencing approaches.

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis.

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g.

Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode and a Promoter Motif Associated with Effector Genes.

Root-knot nematodes (genus ) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes.

Recent applications of biotechnological approaches to elucidate the biology of plant-nematode interactions.

Plant-parasitic nematodes are a major threat to food security. The most economically important species have remarkable abilities to manipulate host physiology and immunity. This review highlights recent applications of biotechnological approaches to elucidate the underlying biology on both sides of the interaction.

Plant-nematode interactions.

Plant-parasitic nematodes threaten food security in the developed and developing world. This review looks at the field through a wide lens, aiming to capture a breadth of recent landmark achievements that have changed our understanding of plant-nematode interactions in particular, and plant pathology in general. It recognises the importance of expanding existing paradigms in plant-pathology to encompass plant-nematode interactions and, at the same time, celebrates achievements that build on the uniqueness of the system.

Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles.

Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations and reverse genetics is entirely reliant on RNA interference.

How Do Pathogens Evolve Novel Virulence Activities?

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere.

A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans.

Background: The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecular mechanisms employed by this nematode to promote virulence remain largely unknown.

Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari.

Interactions between plant-parasitic nematodes and their hosts are mediated by effectors, i.e. secreted proteins that manipulate the plant to the benefit of the pathogen.

The draft genome of .

is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU. is a devastating pest to many crops worldwide.

A genomic resource for the sedentary semi-endoparasitic reniform nematode, Linford & Oliveira.

The reniform nematode () is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here, the authors present a draft genome assembly of . using small- and large-insert libraries sequenced on the Illumina GAIIx and MiSeq platforms.

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.

Background: Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations.

Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes.

Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi.

Correction to: STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plantparasitic nematode Bursaphelenchus xylophilus.

Following publication of the original article [1], the authors reported that one of the authors' names was erroneously changed during proofing and published incorrectly. In this Correction the incorrect and correct author name are shown. The original publication of this article has been corrected.