Plant Parasitic Nematode Identification in Complex Samples with Deep Learning.

Plant parasitic nematodes are significant contributors to yield loss worldwide, causing devastating losses to every crop species, in every climate. Mitigating these losses requires swift and informed management strategies, centered on identification and quantification of field populations. Current plant parasitic nematode identification methods rely heavily on manual analyses of microscope images by a highly trained nematologist. This mode is not only expensive and time consuming, but often excludes the possibility of widely sharing and disseminating results to inform regional trends and potential emergent issues. This work presents a new public dataset containing annotated images of plant parasitic nematodes from heterologous soil extractions. This dataset serves to propagate new automated methodologies or speedier plant parasitic nematode identification using multiple deep learning object detection models and offers a path towards widely shared tools, results, and meta-analyses.

Root-Knot-Nematode-Encoded CEPs Increase Nitrogen Assimilation.

C-terminally encoded peptides (CEPs) are plant developmental signals that regulate growth and adaptive responses to nitrogen stress conditions. These small signal peptides are common to all vascular plants, and intriguingly have been characterized in some plant parasitic nematodes. Here, we sought to discover the breadth of root-knot nematode (RKN)-encoded CEP-like peptides and define the potential roles of these signals in the plant-nematode interaction, focusing on peptide activity altering plant root phenotypes and nitrogen uptake and assimilation. A comprehensive bioinformatic screen identified 61 CEP-like sequences encoded within the genomes of six root-knot nematode (RKN; Meloidogyne spp.) species. Exogenous application of an RKN CEP-like peptide altered A. thaliana and M. truncatula root phenotypes including reduced lateral root number in M. truncatula and inhibited primary root length in A. thaliana. To define the role of RKN CEP-like peptides, we applied exogenous RKN CEP and demonstrated increases in plant nitrogen uptake through the upregulation of nitrate transporter gene expression in roots and increased 15N/14N in nematode-formed root galls. Further, we also identified enhanced nematode metabolic processes following CEP application. These results support a model of parasite-induced changes in host metabolism and inform endogenous pathways to regulate plant nitrogen assimilation.

First Description of the Nuclear and Mitochondrial Genomes and Associated Host Preference of Trichopoda pennipes, a Parasitoid of Nezara viridula.

Trichopoda pennipes is a tachinid parasitoid of several significant heteropteran agricultural pests, including the southern green stink bug, Nezara viridula, and leaf-footed bug, Leptoglossus phyllopus. To be used successfully as a biological control agent, the fly must selectively parasitize the target host species. Differences in the host preference of T. pennipes were assessed by assembling the nuclear and mitochondrial genomes of 38 flies reared from field-collected N. viridula and L. phyllopus. High-quality de novo draft genomes of T. pennipes were assembled using long-read sequencing. The assembly totaled 672 MB distributed among 561 contigs, having an N50 of 11.9 MB and a GC of 31.7%, with the longest contig at 28 MB. The genome was assessed for completeness using BUSCO in the Insecta dataset, resulting in a score of 99.4%, and 97.4% of the genes were single copy-loci. The mitochondrial genomes of the 38 T. pennipes flies were sequenced and compared to identify possible host-determined sibling species. The assembled circular genomes ranged from 15,345 bp to 16,390 bp and encode 22 tRNAs, two rRNAs, and 13 protein-coding genes (PCGs). There were no differences in the architecture of these genomes. Phylogenetic analyses using sequence information from 13 PCGs and the two rRNAs individually or as a combined dataset resolved the parasitoids into two distinct lineages: T. pennipes that parasitized both N. viridula and L. phyllopus, and others that parasitized only L. phyllopus.

A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata) shows highly conserved melanin synthesis pathway genes.

The sphinx moth genus Hyles comprises 29 described species inhabiting all continents except Antarctica. The genus diverged relatively recently (40-25 MYA), arising in the Americas and rapidly establishing a cosmopolitan distribution. The whitelined sphinx moth, Hyles lineata, represents the oldest extant lineage of this group and is one of the most widespread and abundant sphinx moths in North America. Hyles lineata exhibits the large body size and adept flight control characteristic of the sphinx moth family (Sphingidae), but it is unique in displaying extreme larval color variation and broad host plant use. These traits, in combination with its broad distribution and high relative abundance within its range, have made H. lineata a model organism for studying phenotypic plasticity, plant-herbivore interactions, physiological ecology, and flight control. Despite being one of the most well-studied sphinx moths, little data exist on genetic variation or regulation of gene expression. Here, we report a high-quality genome showing high contiguity (N50 of 14.2 Mb) and completeness (98.2% of Lepidoptera BUSCO genes), an important first characterization to facilitate such studies. We also annotate the core melanin synthesis pathway genes and confirm that they have high sequence conservation with other moths and are most similar to those of another, well-characterized sphinx moth, the tobacco hornworm (Manduca sexta).

Temporally Regulated Plant-Nematode Gene Networks Implicate Metabolic Pathways.

Root-knot nematodes (RKN) (Meloidogyne spp.) constantly communicate with their host to establish and maintain specialized feeding cells. They likely regulate this interaction by monitoring host biology. As plant host biology is influenced by light and gene expression varies correspondingly, RKN gene transcription and biology likely follow similar patterns. We profiled RKN transcripts over a period of 24 h and identified approximately 1,000 differentially expressed genes (DEG) in nematode and model host Medicago truncatula, with the majority of DEG occurring in the middle of the dark period. Many of the plant DEG are involved in defense-response pathways, while the nematode DEG are involved in establishing infection, suggesting a strong host-nematode interaction occurring during the dark. To identify interacting genes, we developed a plant-nematode gene network based on DEG signals. The phenylpropanoid pathway was identified as a significant plant-nematode interacting pathway, representing four of 33 genes in the network. We further examined if this pathway interacts similarly in another host, tomato, by quantifying phenolic and flavonoid compounds produced by this pathway. Phenolic compounds showed a significant increase in production during the day in uninoculated plants as compared with during the night. However, during the dark period, there was an increase in flavonoid content in infected plants when compared with uninfected controls, indicating potential host defense mechanisms active during the height of nematode activity at night. This study elucidated cross-species interacting pathways that could be targeted to develop novel management strategies to these important pests.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode.

Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.

Root-knot nematodes demonstrate temporal variation in host penetration.

Root-knot nematodes (RKN; Meloidogyne spp.) are obligate plant parasites that require constant communication with their host to establish and maintain specialized feeding cells. The intimacy of this interaction likely requires constant monitoring of host biology and behavior. As plant processes follow tightly regulated circadian and diurnal patterns, RKN may use similar cues to regulate aspects of this symbiosis. We interrogated RKN biology within the context of host diurnal rhythms throughout nematode development. At 24-hr post-inoculation, RKN penetrated host roots significantly more when inoculated during the night compared to the day. We excluded the possibility that this phenomenon is due to nematode perception of light penetrating the soil, as an identical phenomenon is observed under inverted light conditions. Additionally, when plants were allowed to equilibrate and adjust their light-driven clock under constant light conditions, the temporal variation in nematode penetration was abolished. This phenomenon is not present during earlier nematode developmental stages as egg hatch and infective juvenile mobility did not follow rhythmic patterns and are not affected by light. Taken together, it appears nematode host seeking and penetration are at least partially influenced by daily changes in plant root signaling and light does not have a direct effect on RKN developmental stages. Understanding the role and origin of circadian and diurnal rhythms in the plant-nematode interaction underscores the importance of exploiting basal plant biology to develop novel control methods for these pathogens.Root-knot nematodes (RKN; Meloidogyne spp.) are obligate plant parasites that require constant communication with their host to establish and maintain specialized feeding cells. The intimacy of this interaction likely requires constant monitoring of host biology and behavior. As plant processes follow tightly regulated circadian and diurnal patterns, RKN may use similar cues to regulate aspects of this symbiosis. We interrogated RKN biology within the context of host diurnal rhythms throughout nematode development. At 24-hr post-inoculation, RKN penetrated host roots significantly more when inoculated during the night compared to the day. We excluded the possibility that this phenomenon is due to nematode perception of light penetrating the soil, as an identical phenomenon is observed under inverted light conditions. Additionally, when plants were allowed to equilibrate and adjust their light-driven clock under constant light conditions, the temporal variation in nematode penetration was abolished. This phenomenon is not present during earlier nematode developmental stages as egg hatch and infective juvenile mobility did not follow rhythmic patterns and are not affected by light. Taken together, it appears nematode host seeking and penetration are at least partially influenced by daily changes in plant root signaling and light does not have a direct effect on RKN developmental stages. Understanding the role and origin of circadian and diurnal rhythms in the plant­nematode interaction underscores the importance of exploiting basal plant biology to develop novel control methods for these pathogens.

Suppression of Root-Knot Nematode by Vermicompost Tea Prepared From Different Curing Ages of Vermicompost.

Suppression of root-knot nematodes (Meloidogyne spp.) by vermicompost tea (VCT) has been inconsistent. Greenhouse and laboratory trials were conducted to compare the effects of VCT prepared from different curing ages of vermicompost (VC) on root penetration, reproduction, and hatching of M. incognita. In the penetration experiment, zucchini (Cucurbita pepo) seedlings were drenched with VCT prepared from (i) uncured (UVC), (ii) partially cured (PVC), (iii) completely cured (CVC) vermicompost, and (iv) water or no vermicompost (NVC) 3 days prior to M. incognita inoculation. The experiment was repeated twice on cucumber (Cucumis sativus) and terminated one week after nematode inoculation. All three trials showed that UVC and PVC reduced (P ≤ 0.05) penetration of M. incognita compared with CVC and NVC. Two greenhouse trials showed that VCT from different curing ages of VC did not reduce the abundance of M. incognita juveniles in soil and eggs in roots 2.5 months after nematode inoculation. Two laboratory trials to examine hatching consistently showed that VCT from UVC and PVC suppressed hatching (P ≤ 0.05) compared with NVC, achieving 83.1% hatch reduction by UVC. Overall, VCT from UVC and PVC suppressed root penetration and hatching, but not the reproduction of M. incognita over time.