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Common bean (Phaseolus vulgaris L.) is a crop rich in protein, minerals, and starch. Viruses are a significant limiting factor in increasing the production of legumes, particularly common beans. Accurate and timely detection of plant viruses is essential for minimizing disease damage and ensuring food security. To investigate common bean field viruses in Iran, 300 samples of common bean plants showing viral-like symptoms were collected over 3 years, 2020, 2021, and 2022. This study is the first to use total RNA-seq for a virome analysis of common beans in Iran. The results of the total RNA-seq indicated that the common bean samples were infected with sesame curly top virus (SeCTV), beet curly top Iran virus (BCTIV), tomato leaf curl Palampur virus (ToLCPalV), cucumber mosaic virus (CMV), bean common mosaic virus (BCMV), phaseolus vulgaris endornavirus 1 (PvEV1) and phaseolus vulgaris endornavirus 2 (PvEV2). This is the first report of PvEV1 and PvEV2 in Iran. Moreover, these findings revealed the presence of SeCTV and ToLCPalV for the first time in the western part of the country. Furthermore, the analysis of the nucleotide sequences and the phylogeny tree obtained from the complete genome of the two BCTIV isolates in this study, compared to other isolates, indicated the presence of a new strain of BCTIV in the common bean fields. During the three-year study, the detection rate of viruses indicated that BCTIV and BCTV were more prevalent in Lorestan province than in Markazi province. The research findings showed that common bean fields in the central and western regions of the country were infected with seven viruses, with DNA viruses being more prevalent in Lorestan province than in Markazi province. This information should be taken into account when developing management strategies and breeding plans., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Nothotylenchus savadkoohensis n. sp. was recovered from rotten wood samples of an unidentified forest tree in the Mazandaran province and described herein. It is mainly characterized by an elongated conoid tail ending in a sharply pointed tip and four lines in the lateral field. Females of the new species have 379-662 μm long bodies with 5.8-6.9 μm long stylets ending in fine posteriorly sloping knobs, the metacorpus not valvate, the pharyngeal bulb slightly overlapping the intestine, and the vulva at 76.5-84.0% of body length. Males are also common and have 13.0-14.5 μm long spicules and bursa cloacal. By having an elongated conoid tail and four lines in the lateral field, the new species comes close to four known species, namely N. acris, N. acutus, N. antricolus , and N. truncatus . The morphological differences between the new species and the abovementioned species are discussed. The new species was sequenced for its D2-D3 segment of LSU and ITS rDNA regions. In the LSU phylogenetic tree, the currently available LSU sequences of the genus Nothotylenchus occupied distant placements from each other and the LSU sequence of the new species formed clade with a sequence assigned to Neotylenchus sp. In ITS phylogeny, the newly generated sequence of the new species formed a clade with a clade that includes sequences of Ditylenchus sp. and Neomisticius platypi and N. variabilis ., (© 2024 Soheila Rezaei et al., published by Sciendo.)

In a continuously changing and challenging environment, passing down the memory of encountered stress factors to offspring could provide an evolutionary advantage. In this study, we demonstrate the existence of "intergenerational acquired resistance" in the progeny of rice (Oryza sativa) plants attacked by the belowground parasitic nematode Meloidogyne graminicola. Transcriptome analyses revealed that genes involved in defense pathways are generally downregulated in progeny of nematode-infected plants under uninfected conditions but show a stronger induction upon nematode infection. This phenomenon was termed "spring loading" and depends on initial downregulation by the 24-nucleotide (nt) siRNA biogenesis gene dicer-like 3a (dcl3a) involved in the RNA-directed DNA methylation pathway. Knockdown of dcl3a led to increased nematode susceptibility and abolished intergenerational acquired resistance, as well as jasmonic acid/ethylene spring loading in the offspring of infected plants. The importance of ethylene signaling in intergenerational resistance was confirmed by experiments on a knockdown line of ethylene insensitive 2 (ein2b), which lacks intergenerational acquired resistance. Taken together, these data indicate a role for DCL3a in regulating plant defense pathways during both within-generation and intergenerational resistance against nematodes in rice., Competing Interests: Conflict of interest statement. None declared., (© American Society of Plant Biologists 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Root-knot nematodes (RKN) cause considerable economic losses to kiwifruit production annually. Screening of resistant cultivars has been one of the long-standing methods to manage root-knot nematodes. Here, the reaction of the four most common commercial cultivars of kiwifruit, namely, Actinidia chinensis var. deliciosa cv. Hayward, A. chinensis var. deliciosa cv. Abbott, A. chinensis var. deliciosa cv. Bruno, and A. chinensis var. chinensis cv. Haegeum (commonly known as 'Golden' kiwifruit) to infection by the RKN, Meloidogyne incognita , was evaluated. Among examined cultivars 'Golden' was the most susceptible, having on average 52.8 galls, 56.1 egg masses per gram of root, and 642 J2 population per 200 gram of soil. 'Bruno' showed the highest resistance, with 3.3 galls, 4.1 egg masses per gram of root, and 79 J2 in 200 g of soil. Then, two potential biological control agents, namely Priestia megaterium 31.en and Agrobacterium tumefaciens 19.en were used on 'Hayward' seedlings against M. incognita and showed a significant reduction in the number of galls and egg masses on roots, juvenile population in the soil, and increased the growth parameters of the plants compared to non-treated seedlings. We demonstrated that integrated management using resistant cultivars and biological control can provide a safe and economic method to control RKN, and these resistant cultivars can be used in breeding programs., (© 2023 Seyedeh Najmeh Banihashemian et al., published by Sciendo.)

During a nematological survey in southern Iran, a population belonging to the family Tylenchidae was recovered from a tomato field in Bushehr province. The recovered population belongs to the genus Filenchus, was described and illustrated herein as F. multistriatus n. sp. It is mainly characterized by having a wide and low annulated lip region continuous with adjacent body; amphidial openings confined to the labial plate; four lines in lateral fields forming three bands, with the two outer bands broken by transverse, and the inner one broken by both transverse and longitudinal lines; and median bulb oval with visible valve and elongate-conoid tail uniformly and gradually narrowing toward the distal region, ending in a widely rounded tip. Its morphological and morphometric differences with three closely similar species were discussed. The phylogenetic relationships of the new species with other relevant genera and species were reconstructed using partial sequences of small, and large subunit ribosomal DNA (SSU and LSU rDNA) sequences. Morphometric and morphological data were also provided for an Iranian population of F. sandneri recovered from Bushehr province. Both populations were characterised using SEM data., (© 2023 Somayeh Monemi et al., published by Sciendo.)

A new species of the genus Boleodorus , recovered from southern Iran, is described and illustrated based upon morphological and molecular data. B. bushehrensis n. sp. is mainly characterized by having a wide and low cephalic region (which is continuous with the adjacent body), the oral aperture in a depression in side view under a light microscope, four lines in the lateral field, weak metacorpus with a vestigial-to-invisible valve, and short (26-38 mm long) hooked tail with rounded tip. The females are 334-464 mm long and have a spherical spermatheca filled with spheroid sperm; males have 11.5- to 12.0-mm-long spicules and weakly developed bursa. The new species has an annulated low cephalic region, four large cephalic papillae, and small crescent-shaped amphidial openings when observed by scanning electron microscopy (SEM). Its morphological and morphometric differences with seven known species are discussed. The phylogenetic relationships of the new species with other relevant genera and species have been studied using partial sequences of small and large subunit ribosomal DNA (SSU and LSU rDNA). In both the SSU and LSU phylogenies, the sequences of B . bushehrensis n. sp. and other Boleodorus spp. formed a clade. A second species, B. thylactus , when studied under SEM, has a raised, smooth cephalic region, four large cephalic papillae, and oblique amphidial slits, with the oral opening in a depression., (© 2022 Somayeh Monemi et al., published by Sciendo.)

Background: Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues., Results: We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data., Conclusions: To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies., (© 2021. The Author(s).)

Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone-modifying enzymes have been observed to be deregulated in galls induced by root-knot nematodes (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact has not been comprehensively investigated. First, the role of histone modifications in plant-nematode interactions was confirmed by pharmacological inhibition of histone-modifying enzymes, which all significantly affected rice susceptibility to RKN. For a more specific view, three histone marks, H3K9ac, H3K9me2, and H3K27me3, were subsequently studied by chromatin-immunoprecipitation-sequencing on RKN-induced galls at 3 days postinoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence-related genes. Transcriptome analysis using RNA-Seq and RT-qPCR-based validation revealed that genes marked with H3K9ac or H3K9me2 showed the expected activation or repression gene expression pattern, but this was not the case for H3K27me3 marks. Our results indicate that histone modifications respond dynamically to RKN infection, and that posttranslational modifications mainly at H3K9 specifically target plant defence-related genes., (© 2021 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.)

This contribution provides the morphological and molecular identification of a new species of the genus Longidorella ( Saevadorella ). L. (S.) caspica n. sp., was recovered from the rhizospheric soil of grasses in Mazandaran province in the seashore of the Caspian Sea. It is characterized by females with a length of 788 to 874 μm and a cephalic region with prominent papillae; and separated from the rest of the body by a remarkable constriction, an odontostyle of 32 to 33 μm, vulva at 52.5 to 59.0%, and a tail of 33 to 38 μm with a rounded tip. Males have 32 to 35 μm long spicules of dorylaimoid form and five to seven ventral supplements ending at 48 to 55 μm distance from cloacal pair. The new species was morphologically compared with seven nominal species viz. L. (S.) arenicola, L. (S.) cuspidata, L. (S.) magna, L. (S.) perplexa, L. (S.) saadi , L. ( S .) saevae , and L. (S.) tharensis . It was further compared with similar species under the subgenus Longidorella (Enchodorella) viz. L. (E.) deliblatica and L. (E.) murithi. Besides morphological studies, molecular phylogenetic studies using partial sequences of D2 to D3 expansion fragments of 28S rDNA were performed for the new species and its phylogenetic relationships with other species and genera were discussed., (© 2021 Authors.)

A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants., (© 2020 The Authors. New Phytologist © 2020 New Phytologist Trust.)

Discopersicus iranicus n. gen., n. comb., previously described from Iran as a new species under the genus Discotylenchus , is illustrated using light microscope and scanning electron microscope (SEM) observations and further studied using molecular characters. SEM studies revealed the newly proposed genus has oblique amphidial apertures on the lateral sides of the lip region. SEM images are also provided for two species of Discotylenchus , namely D. discretus and D. brevicaudatus , as the first SEM study of the genus . These results confirmed longitudinal amphidial aperture type on lateral sides of the lip region in genus Discotylenchus , as noted by Siddiqi while erecting the genus with D. discretus as the type species . Molecular phylogenetic analyses using partial small subunit (SSU) and large subunit (LSU) rDNA sequences revealed the affinity of the genus Discopersicus n. gen. with members of the subfamily Boleodorinae, as supported by morphological characters (mainly, the oblique amphidial opening).

Heterodorus youbertghostai n. sp. is described and illustrated based on morphological, morphometric, and molecular data. The new species was found in two geographically distant points in northwestern Iran and is characterized by having angular lip region, separated from the rest body by a constriction, body length of 1,432.5 to 1,751.3 µm, odontostyle length of 24 to 28 µm, rod-like odontophore, 37.0 to 42.5 µm long, lacking flanges at base, double guiding ring at 14 to 16 µm distance from anterior end, pharyngeal bulb comprising 40% to 48% of pharynx, intestine usually containing green material, female reproductive system amphidelphic with less divided short uterus, specific structure of pars distalis vaginae, bluntly conical tail, dorsally convex and ventrally flat, with rounded tip and saccate bodies in ventral side. The new species comes more close to H. conicaudatus and H. irregularis by its morphology and morphometric characters. Compared to former, it has remarkable difference in vulva position and tail characters, and compared to the latter, it could be separated by shorter body, posteriorly located vulva, wider lip region, and longer tail. In phylogenetic analyses using partial sequences of 28S rDNA D2-D3, the new species formed a fully supported clade with several isolates of H. brevidentatus, prevalent in Iran. The other nordiid taxon, Enchodorus dolichurus, already reported from Iran, was also sequenced for the same genomic region and included in phylogenetic analyses.