Beta vulgaris ssp. vulgaris (sugar beet) is one of two plants globally from which sugar is widely produced, accounting for 55% of U.S. sugar $1B (U.S.) and 35% of global raw sugar $4.6B), annually. Its top pathogen, Tetanops myopaeformis, is capable of causing total crop failure, making its study of utmost urgency. A B. vulgaris protease inhibitor, BvSTI (DV501688), one of 22 of its Kunitz trypsin inhibitors (KTIs) that target trypsin (Trp), is expressed during resistance to T. myopaeformis infection. The T. myopaeformis genome made BLASTp searches possible using the Trp protein XP_014094233 from the dipteran Bactrocera oleae, identifying 9 T. myopaeformis Trps then used in Trp docking and cleavage studies. Trp docking analyses using the T. myopaeformis and Trp cleavage studies were done to determine the extent the B. vulgaris resistance architecture could be susceptible to Trp cleavage. KTI protein homologs then were identified in the model agricultural crop Glycine max (soybean) which undergoes infection by the root pathogen Heterodera glycines (soybean cyst nematode) that is used to better understand the B. vulgaris-T. myopaeformis pathosystem. The predicted interactions between G. max KTIs and H. glycines Trps are presented, including GmKTI20, and GmKTI30 that suppress parasitism by > 80%.

Sugar beet (Beta vulgaris ssp. vulgaris), SB, is one of two plants from which sugar is broadly extracted, annually accounting for 55% of U.S. sugar ($1B, U.S.), and 35% global raw sugar ($4.6B). The sugar beet cDNA DV501688, encoding a serine threonine protease inhibitor (BvSTI) was shown to have increased relative transcript abundance in sugar beet during a resistant reaction to the Dipteran sugar beet root maggot, Tetanops myopaeformis SBRM, pest. BLASTp searches of the sugar beet proteome identified 21 additional proteins, each having homology to Kunitz trypsin inhibitors (KTIs) with BvSTI annotated as BvKTI1. Prior deep learning analyses predicted that BvKTI1 bound each of the 9 T. myopaeformis trypsins in the predicted binding loop region located between β-strands 4 and 5 of KTI proteins. The identification of 21 additional BvKTI proteins suggested the plant-insect pest interaction may be more complex, requiring further analysis. The deep learning analysis presented here, using AlphaFold, suggeststhe different BvKTIs may not be equally effective in binding the T. myopaeformis trypsins. BvKTI13 is predicted to bind all 9 T. myopaeformis trypsins with high confidence interface predicted template modelling (ipTM) scores between 0.77 and 0.82. In contrast, BvKTI14, BvKTI20, and BvKTI22 are predicted to not bind any of them (ipTM scores < 0.6). The remaining BvKTIs are predicted to have intermediate capabilities to bind T. myopaeformis trypsins, having predicted binding for some and lacking predicted binding for the others. However, the AlphaFold-based results are predictive and not scientific justification/evidence.

Sugar beet (Beta vulgaris ssp. vulgaris) is one of two plants from which sugar is broadly produced, accounting for 55% of U.S. sugar ($1B, U.S.) and 35% global raw sugar ($4.6B), annually. The sugar beet root maggot (Tetanops myopaeformis) is its top pathogen in the U.S., and capable of causing total crop failure, making its study of urgent need. A B. vulgaris protease inhibitor, BvSTI (DV501688), one of 22 of its Kunitz trypsin inhibitors (KTIs) was shown through deep learning analyses to bind 9 different T. myopaeformis trypsins (Trps). As a surrogate crop experimental system to understand resistance in the B. vulgaris-T. myopaeformis pathosystem, transgenic analysis identified homologous Glycine max (soybean) KTIs expressed in root cells undergoing resistance to its most important pathogen, Heterodera glycines and suppresses parasitism by greater than 80%. The study adds to a list of 114 soybean genes identified in laser microdissection-assisted analyses whose expression suppresses H. glycines parasitism. Deep learning analyses demonstrate the predicted interaction between 2 different H. glycines Trps and each of the 114 defense proteins. Predicted interactions include proteins functioning in the circadian clock, pathogen activated molecular pattern (PAMP)-triggered immunity (PTI), nodulation, salicylic acid-mediated defense processes, cell wall metabolism, and vesicle transport including an alpha soluble NSF attachment protein homolog found at the Rhg1 locus. BLASTp analyses of the B. vulgaris proteome with all 114 G. max defense proteins identified the sugar beet homologs as a pool of potential candidate genes to be employed to generate durable resistance to T. myopaeformis.

The Glycine max (soybean) secretory pathway performs important roles during the defense response to Heterodera glycines parasitism. However, the involvement of some aspects of the secretory machinery remains unexamined. The Sec61 complex of the eukaryote secretory pathway is composed of Sec61-alpha, Sec61-beta, and Sec61-gamma which bind, forming a trimeric complex that imports proteins into the ER for their processing, transport, and secretion. Comparative analyses using Saccharomyces cerevisiae Sec61-alpha, Sec61-beta, and Sec61-gamma protein sequences show G. max has homologs of each, 4 Sec61-alpha, 6 Sec61-beta, and 4 Sec61-gamma paralogs. At least one paralog from each gene family is expressed in H. glycines-parasitized G. max root cells during its defense process. GmSec61-alpha, GmSec61-beta, and GmSec61-gamma overexpression in the H. glycines-susceptible G. max[Williams 82/PI 518671] leads to an engineered defense response. In contrast, RNAi of GmSec61-alpha, GmSec61-beta, and GmSec61-gamma in the H. glycines-resistant G. max[Peking/PI 548402] generates susceptibility. The combined opposite outcomes of GmSec61 overexpression and RNAi provide evidence that they function in the defense process, consistent with the hypothesis that the G. max secretion system plays a role in its defense to H. glycines parasitism. The identification of Sec61-alpha, Sec61-beta, and Sec61-gamma homologs in 51 additional flowering plants spanning 20 Orders and 26 Families including the agriculturally-important Beta vulgaris ssp. vulgaris (sugar beet) demonstrates a potentially broad defense role not limited to these plant species. Computational studies identified genes encoding proteins having signal peptides in B. vulgaris parasitized by H. schachtii but undergoing a defense response further demonstrating the importance of Sec61 translocon in resistance.

Tetanops myopaeformis, the sugar beet root maggot (SBRM), is a devastating insect pathogen of sugar beet, one of only two plants in the world from which sugar is widely produced, accounting for 55% of U.S. sugar and 35% of global raw sugar with an annual farm value of $3 billion in the United States. T. myopaeformis is capable of causing total crop failure, making its study important. The previously released SBRM genome, TmSBRM_v1.0, has been generated from the de novo assembled draft genome sequence of T. myopaeformis isolated that was isolated from field-grown B. vulgaris in North Dakota, USA. The annotation of the T. myopaeformis is presented here. The annotated T. myopaeformis genome should be useful in understanding the biology of this insect and the development of new control strategies for this pathogen, relationship to model genetic organisms like Drosophila melanogaster and aid in agronomic improvement of sugar beet for stakeholders while also providing information on the relationship between the SBRM and climate change.

Sugar beet (SB), Beta vulgaris ssp, vulgaris (B. vulgaris), is one of only two plants in the world from which significant amounts of raw sugar is produced. This value of sugar, derived from SB, is 55% in the United States and 35% of global raw sugar with an annual farm worth in the U.S. alone of $1B, $4.6B globally. Tetanops myopaeformis (von Röder), the sugar beet root maggot (SBRM), is a devastating insect pathogen of SB and the most devastating SB pathogen in North America, decreasing production by up to 100%. The T. myopaeformis TmSBRM_v1.0 draft genome has been generated from DNA isolated from field-grown B. vulgaris from North Dakota, USA. A genome database for the annotated T. myopaeformis TmSBRM_v1.0 draft genome, SBRM database, has been generated and is presented here with the aim of aiding in agronomic improvement of SB for stakeholders.

The sugar beet root maggot (SBRM), Tetanops myopaeformis (von Röder) insect pathogen devastates sugar beet (SB), Beta vulgaris ssp, vulgaris (B. vulgaris), one of only two plants from which significant global raw sugar is produced, $1B, U.S., $4.6 B, globally. Larval SBRMs experiencing F1010 and L19 susceptible or F1016 and F1024 resistant SB responses are RNA sequenced, sampled at time = 0 hours post infection [hpi], 24, 48 and 72 hpi. Transcriptomic analyses determined the number of reads per sample, mapped the transcripts to the recently sequenced SBRM TmSBRM_v1.0 draft genome and identified genes that relate to the resistant and susceptible responses. The RNA-seq study provides data for generating differential expression analyses, yielding an understanding SBRM biology, control strategy development, relationship to model and non-model organisms and aiding sugar beet improvement for stakeholders.

Pathogen-secreted polygalacturonases (PGs) alter plant cell wall structure by cleaving the α-(1→4) linkages between D-galacturonic acid residues in homogalacturonan (HG), macerating the cell wall, facilitating infection. Plant PG inhibiting proteins (PGIPs) disengage pathogen PGs, impairing infection. The soybean cyst nematode, Heterodera glycines, obligate root parasite produces secretions, generating a multinucleate nurse cell called a syncytium, a byproduct of the merged cytoplasm of 200-250 root cells, occurring through cell wall maceration. The common cytoplasmic pool, surrounded by an intact plasma membrane, provides a source from which H. glycines derives nourishment but without killing the parasitized cell during a susceptible reaction. The syncytium is also the site of a naturally-occurring defense response that happens in specific G. max genotypes. Transcriptomic analyses of RNA isolated from the syncytium undergoing the process of defense have identified that one of the 11 G. max PGIPs, GmPGIP11, is expressed during defense. Functional transgenic analyses show roots undergoing GmPGIP11 overexpression (OE) experience an increase in its relative transcript abundance (RTA) as compared to the ribosomal protein 21 (GmRPS21) control, leading to a decrease in H. glycines parasitism as compared to the overexpression control. The GmPGIP11 undergoing RNAi experiences a decrease in its RTA as compared to the GmRPS21 control with transgenic roots experiencing an increase in H. glycines parasitism as compared to the RNAi control. Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and effector triggered immunity (ETI) components are shown to influence GmPGIP11 expression while numerous agricultural crops are shown to have homologs.

Sugar beet (SB), Beta vulgaris ssp, vulgaris (B. vulgaris) is one of only two plants in the world from which significant global raw sugar is produced, $1 billion, U.S., $4.6 B, globally. Tetanops myopaeformis (von Roder), the sugar beet root maggot (SBRM), is a devastating insect pathogen that can decrease yield almost completely. Experiments reveal the SBRM larval transcriptome experiencing two different susceptible or resistant responses by sugar beet SBRM larvae were sampled at time = 0 hours post infection [hpi]), prior to being introduced to B. vulgaris and after infection on F1016 and F1024 (resistant), and F1010 and L19 (susceptible) for 24, 48, and 72 hpi when the larvae were removed for transcriptomic analysis. The transcriptomic analyses included determining the number of reads per sample, mapping the transcripts to the recently sequenced SBRM TmSBRM_v1.0 draft genome, identifying genes that relate to the resistant and susceptible responses. Moreover, the RNA-seq experiments provide data for generating differential expression analyses between the various sample types, thus, yielding an understanding SBRM biology, the development of new control strategies for this pathogen, relationship to model genetic organisms like Drosophila melanogaster, relationship to pathogenic non-model organisms, and aid in agronomic improvement of sugar beet for stakeholders. ### Competing Interest Statement The authors have declared no competing interest.

Supplementary Methods, Figures 1-4, Tables 1-5 from The mRNA-Destabilizing Protein Tristetraprolin Is Suppressed in Many Cancers, Altering Tumorigenic Phenotypes and Patient Prognosis

The plant cell wall structure can be altered by pathogen-secreted polygalacturonases (PGs) that cleave the α-(1→4) linkages occurring between D-galacturonic acid residues in homogalacturonan. The activity of the PGs leads to cell wall maceration, facilitating infection. Plant PG inhibiting proteins (PGIPs) impede pathogen PGs, impairing infection and leading to the ability of the plant to resist infection. Analyses show the Glycine max PGIP11 (GmPGIP11) is expressed within a root cell that is parasitized by the pathogenic nematode Heterodera glycines, the soybean cyst nematode (SCN), but while undergoing a defence response that leads to its demise. Transgenic experiments show GmPGIP11 overexpression leads to a successful defence response, while the overexpression of a related G. max PGIP, GmPGIP1 does not, indicating a level of specificity. The analyses presented here have identified PGIPs from 51 additional studied proteomes, many of agricultural importance. The analyses include the computational identification of signal peptides and their cleavage sites, O-, and N-glycosylation. Artificial intelligence analyses determine the location where the processed protein localize. The identified PGIPs are presented as a tool base from which functional transgenics can be performed to determine whether they may have a role in plant-pathogen interactions.

ABSTRACT The sugar beet root maggot (SBRM), Tetanops myopaeformis (von Röder), is a devastating pathogen of sugar beet (SB), Beta vulgaris , ssp vulgaris ( B. vulgaris ), an important food crop, while also being one of only two plants globally from which sugar is widely produced, and accounting for 35% of global raw sugar with an annual farm value of $3 billion in the United States alone. SBRM is the most devastating pathogen of sugar beet in North America. The limited natural resistance of B. vulgaris necessitates an understanding of the SBRM genome to facilitate generating knowledge of its basic biology, including the interaction between the pathogen and its host(s). Presented is the de novo assembled draft genome sequence of T. myopaeformis isolated from field-grown B. vulgaris in North Dakota, USA. The SBRM genome sequence will also be valuable for molecular genetic marker development to facilitate host resistance gene identification and knowledge, including SB polygalacturonase inhibiting protein (PGIP), and development of new control strategies for this pathogen. SPECIFICATIONS Organism/cell line/tissue: Tetanops myopaeformis Sequencer or array type: PacBio Revio flow cell Data format: Raw and processed Experimental factors: DNA extracted from a wild-type strain, no treatment Experimental features: Genome sequencing Consent n/a Sample source location: Sugar beet field at Fargo, North Dakota, USA DIRECT LINK TO DEPOSITED DATA BioSample accession: SAMN37733483 Temporary Submission ID: SUB13882507 BioProject ID: PRJNA1026092 Release date: 2024-09-09, or with the release of linked data, whichever is first

Expression of the central circadian oscillator components CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), TIMING OF CAB1 (TOC1), GIGANTEA (GI), and CONSTANS (CO) occurs in Glycine max root cells (syncytia) parasitized by the nematode Heterodera glycines while undergoing resistance, indicating a defense role. GmCCA1-1 relative transcript abundance (RTA) in roots experiencing overexpression (OE) or RNA interference (RNAi) is characterized by rhythmic oscillations, compared to a ribosomal protein gene (GmRPS21) control. A GmCCA1-1 RTA change, advancing by 12 h, exists in H. glycines-infected as compared to uninfected controls in wild-type, H. glycines-resistant, G. max[Peking/PI 548402]. The G. max[Peking/PI 548402] transgenic controls exhibit the RTA change by 4 h post infection (hpi), not consistently occurring in the H. glycines-susceptible G. max[Williams 82/PI 518671] until 56 hpi. GmCCA1-1 expression is observed to be reduced in H. glycines-infected GmCCA1-1-OE roots as compared to non-infected transgenic roots with no significant change observed among RNAi roots. The GmCCA1-1 expression in transgenic GmCCA1-1-OE roots remains higher than control and RNAi roots. Decreased GmCCA1-1 mRNA among infected roots shows the altered expression is targeted by H. glycines. Gene expression of proven defense genes including 9 different mitogen activated protein kinases (GmMAPKs), NON-RACE SPECIFIC DISEASE RESISTANCE 1 (GmNDR1-1), RPM1-INTERACTING PROTEIN 4 (GmRIN4-4), and the secreted xyloglucan endotransglycosylase/hydrolase 43 (GmXTH43) in GmCCA1-1-OE and GmCCA1-1-RNAi roots, compared to controls, reveal a significant role of GmCCA1-1 expression in roots undergoing defense to H. glycines parasitism. The observation that GmCCA1-1 regulates GmXTH43 expression links the central circadian oscillator to the functionality of the secretion system.

Two conserved Glycine max (soybean) mitogen activated protein kinase 3 (MAPK3) paralogs function in defense to the parasitic soybean cyst nematode Heterodera glycines. Gene Ontology analyses of RNA seq data obtained from MAPK3-1-overexpressing (OE) and MAPK3-2-OE roots compared to their control, as well as MAPK3-1-RNA interference (RNAi) and MAPK3-2-RNAi compared to their control, hierarchically orders the induced and suppressed genes, strengthening the hypothesis that their heterologous expression in Gossypium hirsutum (upland cotton) would impair parasitism by the root knot nematode (RKN) Meloidogyne incognita. MAPK3-1 expression (E) in G. hirsutum suppresses the production of M. incognita root galls, egg masses, and second stage juveniles (J2s) by 80.32%, 82.37%, and 88.21%, respectfully. Unexpectedly, egg number increases by 28.99% but J2s are inviable. MAPK3-2-E effects are identical, statistically. MAPK3-1-E and MAPK3-2-E decreases root mass 1.49-fold and 1.55-fold, respectively, as compared to the pRAP15-ccdB-E control. The reproductive factor (RF) of M. incognita for G. hirsutum roots expressing MAPK3-1-E or MAPK3-2-E decreases 60.39% and 50.46%, respectively, compared to controls. The results are consistent with upstream pathogen activated molecular pattern (PAMP) triggered immunity (PTI) and effector triggered immunity (ETI) functioning in defense to H. glycines. The experiments showcase the feasibility of employing MAPK3, through heterologous expression, to combat M. incognita parasitism, possibly overcoming impediments otherwise making G. hirsutum's defense platform deficient. MAPK homologs are identified in other important crop species for future functional analyses.

In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.

Glycine max root cells developing into syncytia through the parasitic activities of the pathogenic nematode Heterodera glycines underwent isolation by laser microdissection (LM). Microarray analyses have identified the expression of a G. max DOESN'T MAKE INFECTIONS3 (DMI3) homolog in syncytia undergoing parasitism but during a defense response. DMI3 encodes part of the common symbiosis pathway (CSP) involving DMI1, DMI2, and other CSP genes. The identified DMI gene expression, and symbiosis role, suggests the possible existence of commonalities between symbiosis and defense. G. max has 3 DMI1, 12 DMI2, and 2 DMI3 paralogs. LM-assisted gene expression experiments of isolated syncytia under further examination here show G. max DMI1-3, DMI2-7, and DMI3-2 expression occurring during the defense response in the H. glycines-resistant genotypes G.max [Peking/PI548402] and G.max [PI88788] indicating a broad and consistent level of expression of the genes. Transgenic overexpression (OE) of G. max DMI1-3, DMI2-7, and DMI3-2 impairs H. glycines parasitism. RNA interference (RNAi) of G. max DMI1-3, DMI2-7, and DMI3-2 increases H. glycines parasitism. The combined opposite outcomes reveal a defense function for these genes. Prior functional transgenic analyses of the 32-member G. max mitogen activated protein kinase (MAPK) gene family has determined that 9 of them act in the defense response to H. glycines parasitism, referred to as defense MAPKs. RNA-seq analyses of root RNA isolated from the 9 G. max defense MAPKs undergoing OE or RNAi reveal they alter the relative transcript abundances (RTAs) of specific DMI1, DMI2, and DMI3 paralogs. In contrast, transgenically-manipulated DMI1-3, DMI2-7, and DMI3-2 expression influences MAPK3-1 and MAPK3-2 RTAs under certain circumstances. The results show G. max homologs of the CSP, and defense pathway are linked, apparently involving co-regulated gene expression.

The endomembrane system, functioning in secretion, performs many roles relating to eukaryotic cell physiological processes and the Golgi apparatus is the central organelle in this system. An essential associated Golgi component is the conserved oligomeric Golgi (COG) complex, maintaining correct Golgi structure and function during retrograde trafficking. In animals, naturally occurring cog mutants provide a window into understanding it’s function(s). Eliminating even one COG component impairs its function. In animals, COG mutations lead to severe cell biological and developmental defects and death while far less is understood in plants which is changing. The plant genetic model Arabidopsis thaliana COG complex functions in growth, cell expansion and other processes, involving direct interactions with other secretion system components including the exocyst, soluble N-Ethylmaleimide-Sensitive Factor Attachment Protein Receptor (SNARE), and the microtubule cytoskeleton. Recent experiments have identified a defense role for the COG complex in plants, the focus of this review.

Crop improvement can be facilitated through efficient gene transfer, leading to pRAP plasmid development. Comparative hairy root transformation results from 24 previously published articles examining 29,756 roots show a 70% transformation efficiency. Average gene overexpression was 11.24-fold and −3.84-fold in RNAi roots. New studies show Glycine max BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) overexpression leads to a 67% decrease in Heterodera glycines parasitism while BAK1-1 RNAi led to a 4.8-fold increase in parasitism. The results show pathogen associated molecular pattern triggered immunity (PTI) functions in the G. max-H. glycines pathosystem during defense. Consequently, the pRAP vectors have applicability for studying basic biology and defense in other agricultural plants including Manihot esculenta (cassava), Zea mays (maize), Oryza sativa (rice), Triticum aestivum (wheat), Sorghum bicolor (sorghum), Brassica rapa (rape seed), Solanum tuberosum (potato), Solanum lycopersicum (tomato), Elaes guineensis (oil palm), Saccharum officinalis (sugarcane) and Beta vulgaris (sugar beet) since each have BAK1 homologs.

The conserved oligomeric Golgi (COG) complex maintains correct Golgi structure and function during retrograde trafficking. Glycine max has 2 paralogs of each COG gene, with one paralog of each gene family having a defense function to the parasitic nematode Heterodera glycines. Experiments presented here show G. max COG paralogs functioning in defense are expressed specifically in the root cells (syncytia) undergoing the defense response. The expressed defense COG gene COG7-2-b is an alternate splice variant, indicating specific COG variants are important to defense. Transcriptomic experiments examining RNA isolated from COG overexpressing and RNAi roots show some COG genes co-regulate the expression of other COG complex genes. Examining signaling events responsible for COG expression, transcriptomic experiments probing MAPK overexpressing roots show their expression influences the relative transcript abundance of COG genes as compared to controls. COG complex paralogs are shown to be found in plants that are agriculturally relevant on a world-wide scale including Manihot esculenta, Zea mays, Oryza sativa, Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Brassica rapa, Elaes guineensis and Saccharum officinalis and in additional crops significant to U.S. agriculture including Beta vulgaris, Solanum tuberosum, Solanum lycopersicum and Gossypium hirsutum. The analyses provide basic information on COG complex biology, including the coregulation of some COG genes and that MAPKs functioning in defense influence their expression. Furthermore, it appears in G. max and likely other crops that some level of neofunctionalization of the duplicated genes is occurring. The analysis has identified important avenues for future research broadly in plants.