Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii

Root-knot nematodes (RKN) of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control RKN is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on Meloidogyne enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest requiring regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of M. enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting triploid genome assembly spans 285.4 Mb with 556 contigs, a GC% of 30 ± 0.042 and an N50 value of 2.11 Mb, constituting a useful platform for comparative, population and functional genomics.

Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor

Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogenic mechanisms. Herein, we combined Illumina short reads, PacBio long reads, and Hi-C mapping technology to construct a chromosome-scale reference genome assembly for D. destructor. The genome assembly totals 133.86 Mb, with 129.51 Mb (96.74%) of sequences anchored onto 4 pseudo-chromosomes, achieving a scaffold N50 of 32.25 Mb. The assembled genome contains 28.14% repeat sequences and identifies 19,165 protein-coding genes, of which 18,444 (96.24%) are functionally annotated. The genome assembly demonstrates a high level of completeness, with 73.8% complete the nematoda-specifc Benchmarking Universal Single-Copy Orthologs (BUSCO) genes, significantly higher than that of other reported plant-parasitic nematode genomes. This high-quality reference genome will serve as a valuable genomic resource for future research aimed at understanding the pathogenesis of D. destructor and developing effective control strategies.

Integrative multi-omics analysis reveals the translational landscape of the plant-parasitic nematode Meloidogyne incognita

Root-knot nematodes (RKNs) of the genus Meloidogyne pose the most significant threats to global food security due to their destructive nature as plant-parasitic nematodes. Although significant attention has been devoted to investigating the gene transcription profiling of RKNs, our understanding of the translational landscape of RKNs remains limited. In this study, we elucidated the translational landscape of Meloidogyne incognita through the integration of translatome, transcriptome and quantitative proteome analyses. Our findings revealed numerous previously unannotated translation events and refined the genome annotation. By investigating the genome-wide translational dynamics of M. incognita during parasitism, we revealed that the genes of M. incognita undergo parasitic stage-specific regulation at the translational level. Interestingly, we identified 470 micropeptides (containing fewer than 100 amino acids) with the potential to function as effectors. Additionally, we observed that the effector-coding genes in M. incognita exhibit higher translation efficiency (TE). Further analysis suggests that M. incognita has the potential to regulate the TE of effector-coding genes without simultaneous alterations in their transcript abundance, facilitating effector synthesis. Collectively, our study provides comprehensive datasets and explores the genome-wide translational landscape of M. incognita, shedding light on the contributions of translational regulation during parasitism.

Nematodes exposed to furfural acetone exhibit a species-specific vacuolar H+-ATPase response

Furfural acetone (FAc) is widely used as an additive by the food industry, as well as an intermediate in several fine chemical industries. Its nematicidal activity against the free-living model organism Caenorhabditis elegans and the parasitic nematode Meloidogyne incognita are well known, but its molecular mechanism of action remains unclear. To deep this subject, we performed 48-h lethal tests on eight nematode species, encompassing free-living, plant-parasitic, and animal-parasitic nematodes. Our results revealed that FAc possesses broad-spectrum nematicidal activity, with potent effects against parasitic nematodes such as Strongyloides stercoralis and M. incognita. In contrast, it exhibited weak activity against the free-living nematode C. elegans, suggesting its potential as a selective nematicide. Our investigation unveiled that FAc binds to the vacuolar H+-ATPase subunits VHA-12 and VHA-13, accelerating intestinal cell necrosis and leading to the death of C. elegans. It is the first discovery that VHA-12 and VHA-13 can serve as target proteins for triggering nematode cell necrosis. The interaction results indicated that FAc targets proteins VHA-12 and VHA-13 of different nematodes and confers broad-spectrum nematicidal activity. And the Spearman analysis results illustrated that the differential nematicidal activity of FAc against various nematodes is attributed to variations in the sequence and structure of the receptor proteins VHA-12 and VHA-13 among different nematode species. Our results illuminate the molecular mechanism underlying the differential toxicity of FAc to different nematodes, and provide valuable data for the comprehensive risk assessment of FAc release into the environment.

Root-knot nematodes exploit the catalase-like effector to manipulate plant reactive oxygen species levels by directly degrading H2O2

Plants produce reactive oxygen species (ROS) upon infection, which typically trigger defence mechanisms and impede pathogen proliferation. Root-knot nematodes (RKNs, Meloidogyne spp.) represent highly detrimental pathogens capable of parasitizing a broad spectrum of crops, resulting in substantial annual agricultural losses. The involvement of ROS in RKN parasitism is well acknowledged. In this study, we identified a novel effector from Meloidogyne incognita, named CATLe, that contains a conserved catalase domain, exhibiting potential functions in regulating host ROS levels. Phylogenetic analysis revealed that CATLe is conserved across RKNs. Temporal and spatial expression assays showed that the CATLe gene was specifically up-regulated at the early infection stages and accumulated in the subventral oesophageal gland cells of M. incognita. Immunolocalization demonstrated that CATLe was secreted into the giant cells of the host plant during M. incognita parasitism. Transient expression of CATLe significantly dampened the flg22-induced ROS production in Nicotiana benthamiana. In planta assays confirmed that M. incognita can exploit CATLe to manipulate host ROS levels by directly degrading H2O2. Additionally, interfering with expression of the CATLe gene through double-stranded RNA soaking and host-induced gene silencing significantly attenuated M. incognita parasitism, highlighting the important role of CATLe. Taken together, our results suggest that RKNs can directly degrade ROS products using a functional catalase, thereby manipulating host ROS levels and facilitating parasitism.

Resistance to both aphids and nematodes in tobacco plants expressing a Bacillus thuringiensis crystal protein

BACKGROUND

Bacillus thuringiensis (Bt) and its crystal toxin or δ-endotoxins (Cry) offer great potential for the efficient control of crop pests. A vast number of pests can potentially infect the same host plant, either simultaneously or sequentially. However, no effective Bt-Cry protein has been reported to control both aphids and plant parasitic nematodes due to its highly specific activity.

RESULTS

Our study indicated that the Cry5Ba2 protein was toxic to the green peach aphid Myzus persicae, which had a median lethal concentration (LC50) of 9.7 ng μL-1 and fiducial limits of 3.1-34.6 ng μL-1. Immunohistochemical localization of Cry5Ba2 revealed that it could bind to the apical tip of microvilli in midgut regions. Moreover, transgenic tobacco plants expressing Cry5Ba2 exhibited significant resistance to Myzus persicae, as evidenced by reduced insect survival and impaired fecundity, and also intoxicated the Meloidogyne incognita as indicated by a decrease in galls and progeny reproduction.

CONCLUSION

In sum, we identified a new aphicidal Bt toxin resource that could simultaneously control both aboveground and belowground pests, thus extending the application range of Bt-based strategy for crop protection. © 2024 Society of Chemical Industry.

High-resolution transcriptome datasets during embryogenesis of plant-parasitic nematodes

Understanding the transcriptional regulatory characteristics throughout the embryogenesis of plant-parasitic nematodes is crucial for elucidating their developmental processes' uniqueness. However, a challenge arises due to the lack of suitable technical methods for synchronizing the age of plant-parasitic nematodes embryo, it is difficult to collect detailed transcriptome data at each stage of embryonic development. Here, we recorded the 11 embryonic developmental time-points of endophytic nematode Meloidogyne incognita (isolated from Wuhan, China), Heterodera glycines (isolated from Wuhan, China), and Ditylenchus destructor (isolated from Jinan, China) species, and constructed transcriptome datasets of single embryos of these three species utilizing low-input smart-seq2 technology. The datasets encompassed 11 complete embryonic development stages, including Zygote, 2-cell, 4-cell, 8-cell, 24-44 cell, 64-78 cell, Comma, 1.5-fold, 2-fold, Moving, and L1, each stage generated four to five replicates, resulting in a total of 162 high-resolution transcriptome libraries. This high-resolution cross-species dataset serves as a crucial resource for comprehending the embryonic developmental properties of plant-parasitic nematodes and for identifying functional regulatory genes during embryogenesis.

Chromosome-level genome assembly of the cereal cyst nematode Heterodera flipjevi

As an economically important plant parasitic nematode (PPN), Heterodera filipjevi causes great damage on wheat, and now it was widely recorded in many countries. While multiple genomes of PPNs have been published, high-quality genome assembly and annotation on H. filipjevi have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for H. filipjevi, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The genome consists of 9 pseudo-chromosomes that contain 134.19 Mb of sequence, with a scaffold N50 length of 11.88 Mb. In total, 10,036 genes were annotated, representing 75.20% of the total predicted protein-coding genes. Our study provides the first chromosome-scale genome for H. filipjevi, which is also the inaugural high-quality genome of cereal cyst nematodes (CCNs). It provides a valuable genomic resource for further biological research and pest management of cereal cyst nematodes disease.

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity.

3-(Methylthio)Propionic Acid from Bacillus thuringiensis Berliner Exhibits High Nematicidal Activity against the Root Knot Nematode Meloidogyne incognita (Kofoid and White) Chitwood

Root knot nematodes cause serious damage to global agricultural production annually. Given that traditional chemical fumigant nematicides are harmful to non-target organisms and the environment, the development of biocontrol strategies has attracted significant attention in recent years. In this study, it was found that the Bacillus thuringiensis Berliner strain NBIN-863 exhibits strong fumigant nematicidal activity and has a high attraction effect on Meloidogyne incognita (Kofoid and White) Chitwood. Four volatile organic compounds (VOCs) produced by NBIN-863 were identified using solid-phase microextraction and gas chromatography-mass spectrometry. The nematicidal activity of four VOCs, namely, N-methylformamide, propenamide, 3-(methylthio)propionic acid, and phenylmalonic acid, was detected. Among these compounds, 3-(methylthio)propionic acid exhibited the highest direct contact nematicidal activity against M. incognita, with an LC50 value of 6.27 μg/mL at 24 h. In the fumigant bioassay, the mortality rate of M. incognita treated with 1 mg/mL of 3-(methylthio)propionic acid for 24 h increased to 69.93%. Furthermore, 3-(methylthio)propionic acid also exhibited an inhibitory effect on the egg-hatching of M. incognita. Using chemotaxis assays, it was determined that 3-(methylthio)propionic acid was highly attractive to M. incognita. In pot experiments, the application of 3-(methylthio)propionic acid resulted in a reduction in gall numbers, decreasing the number of galls per gram of tomato root from 97.58 to 6.97. Additionally, the root length and plant height of the treated plants showed significant increases in comparison with the control group. The current study suggests that 3-(methylthio)propionic acid is a novel nematicidal virulence factor of B. thuringiensis. Our research provides evidence for the potential use of NBIN-863 or its VOCs in biocontrol against root knot nematodes.