A small-scale procedure for extracting nucleic acids from woody plants infected with various phytopathogens for PCR assay

Seasonal Dynamics and Distribution of Xylella fastidiosa in Infected Almond Trees

This research focused on studying the dynamics of the bacterial pathogen Xylella fastidiosa in almond trees across different developmental stages. The objective was to understand the seasonal distribution and concentration of X. fastidiosa within almond trees. Different tree organs, including leaves, shoots, branches, fruits, flowers, and roots, from 10 X. fastidiosa-infected almond trees were sampled over 2 years. The incidence and concentration of X. fastidiosa were determined using qPCR and isolation. Throughout the study, X. fastidiosa was consistently absent from fruits, flowers, and roots, whereas it was detected in leaves as well as in shoots and branches. We demonstrate that the absence of X. fastidiosa in the roots is likely linked to the inability of this isolate to infect the peach-almond hybrid rootstock GF677. X. fastidiosa incidence in shoots and branches remained consistent throughout the year, whereas in leaf petioles, it varied across developmental stages, with lower detection during the early and late stages of the season. Similarly, viable X. fastidiosa cells were isolated from shoots and branches at all developmental stages, but no successful isolations were achieved from leaf petioles during the vegetative and nut growth stage. Studying the progression of almond leaf scorch symptoms in trees with initial infections showed that once symptoms emerged on one branch, symptomless branches were likely already infected by the bacterium. Therefore, selectively pruning symptomatic branches is unlikely to cure the tree. This study enhances our understanding of X. fastidiosa dynamics in almond trees and may have practical applications for its detection and control.

Overexpressing CYP81D11 enhances 2,4,6-trinitrotoluene tolerance and removal efficiency in Arabidopsis

Phytoremediation is a promising technology for removing the high-toxic explosive 2,4,6-trinitrotoluene (TNT) pollutant from the environment. Mining dominant genes is the key research direction of this technology. Most previous studies have focused on the detoxification of TNT rather than plants' TNT tolerance. Here, we conducted a transcriptomic analysis of wild type Arabidopsis plants under TNT stress and found that the Arabidopsis cytochrome P450 gene CYP81D11 was significantly induced in TNT-treated plants. Under TNT stress, the root length was approximately 1.4 times longer in CYP81D11-overexpressing transgenic plants than in wild type plants. The half-removal time for TNT was much shorter in CYP81D11-overexpressing transgenic plants (1.1 days) than in wild type plants (t1/2 = 2.2 day). In addition, metabolic analysis showed no difference in metabolites in transgenic plants compared to wild type plants. These results suggest that the high TNT uptake rates of CYP81D11-overexpressing transgenic plants were most likely due to increased tolerance and biomass rather than TNT degradation. However, CYP81D11-overexpressing plants were not more tolerant to osmotic stresses, such as salt or drought. Taken together, our results indicate that CYP81D11 is a promising target for producing bioengineered plants with high TNT removing capability.

Vector transmission of parsley yellow leaf curl virus by the leafhopper Austroagallia sinuata

Parsley yellow leaf curl virus (PYLCV) is a new member of the family Geminiviridae that has not yet been assigned to an established genus due to limited information about its biological properties. In this study, the ability of Austroagallia leafhoppers, which are commonly found on vegetable farms in Kerman province (Iran), to transmit this virus was studied. After a two-day acquisition access period, Austroagallia sp. successfully transmitted the virus from PYLCV-infected parsley to healthy seedlings. On the basis of male genitalia morphology, the species of leafhopper was identified as A. sinuata. This is the first report of a transmission of plant virus by a member of the genus Austroagallia.

Physalis virginiana as a Wild Field Host of Bactericera cockerelli (Hemiptera: Triozidae) and 'Candidatus Liberibacter solanacearum'

The potato/tomato psyllid, Bactericera cockerelli (Šulc), is among the most important pests of solanaceous crops as a vector of the pathogen 'Candidatus Liberibacter solanacearum' (Lso). Lso-infected psyllids often arrive in crop fields from various wild species of Solanaceae and Convolvulaceae, especially those that provide early-season hosts for the vector. Physalis species are perennial plants within the family Solanaceae with often broad geographical distributions that overlap those of B. cockerelli, yet the status of many Physalis species as hosts for B. cockerelli or Lso remains unknown. Our objective was to determine whether wild Physalis species that occur in the potato-growing region of Galeana, Nuevo León, Mexico, host B. cockerelli populations and whether they also are susceptible to Lso. Sampling was carried out in the potato-growing zone of Galeana, Nuevo León, Mexico, where unidentified Physalis spp. are common. In March to October 2021, a wild plant identified as Physalis virginiana was observed; eggs, nymphs, and adults of B. cockerelli were observed on these plants throughout the growing season, and nymphs completed development on these plants under laboratory conditions. Lso also was detected in 22 of the 93 (23.7%) wild P. virginiana plants using conventional PCR, while 13.3% of B. cockerelli adults that emerged from P. virginiana cuttings harbored the pathogen. This is the first report that P. virginiana is a host for B. cockerelli and for Lso. These results suggest that P. virginiana is a likely source of Lso-infected psyllids colonizing solanaceous crops in northeastern Mexico. The importance of P. virginiana and other wild hosts on the population dynamics of the vector and pathogen should be investigated to assist in pest management decision-making.

A high-throughput plate method for nucleic acid extraction from beet leafhopper (Hemiptera: Cicadellidae) and potato psyllid (Hemiptera: Triozidae) for pathogen detection

Plant pathogens that are transmitted by insect vectors cause considerable damage to crops when pests or pathogens are not detected early in the season and populations are not controlled. Knowledge of pathogen prevalence in insect pest populations can aid growers in their insect pest management decisions but requires the timely dissemination of results. This process requires that specimen capture, identification, nucleic acid extraction, and molecular detection of a pathogen(s) occur alongside a platform for sharing results. The potato psyllid (Bactericera cockerelli, Sulc; Hemiptera: Triozidae) and beet leafhopper (Circulifer tenellus, Baker; Hemiptera: Cicadellidae) transmit pathogens to potato and other vegetable or seed crops each season in the northwestern United States. While the potato psyllid has been tested for pathogen occurrence for the past decade, testing of the beet leafhopper is a new endeavor and substantially increases the specimen number that must be tested by our laboratories each season. To aid in the rapid processing of individual insect specimens, we optimized and validated a new high-throughput 96-well plate nucleic acid extraction method for use in place of a standard 1.5-ml single-tube extraction method. Processing efficiency, in terms of total specimens processed over a 2-day period, improved 2.5-fold, and the cost associated with processing a single sample was nearly cut in half with this newly developed plate nucleic acid extraction method. Overall, this method has proven to be an excellent tool for the rapid testing of large numbers of small, individual insect vectors to enable timely dissemination of data on pathogen prevalence to growers.

First report of 'Candidatus Phytoplasma asteris' associated with yellowing, scorching and decline of almond trees in India

The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 'Candidatus Phytoplasma' species globally, among which 'Candidatus Phytoplasma asteris' is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020-2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped 'Prunus dulcis' aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with 'Prunus dulcis' phytoplasma PAEs3 and 'Prunus dulcis' phytoplasma PAE28 from Iran. This research presents the first host report of 'Candidatus Phytoplasma asteris' infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally.

Morphological and molecular characterization of Lasiodiplodia theobromae associated with leaf spot and blight disease of Coscinium fenestratum (Gaertn.) Colebr.-a new host record from India

Coscinium fenestratum is a medicinally significant critically endangered plant found in Western Ghats of India. The leaf spot and blight was observed in Kerala during 2021 with disease incidence of 40% in 20 assessed plants in 0.6 hectare. The associated fungus was isolated on potato dextrose agar medium. A total of six morpho-culturally identical isolates were isolated and morphologically identified. Based on morpho-cultural features, the fungus was identified at genus level as Lasiodiplodia sp., which was further authentically confirmed as Lasiodiplodia theobromae by molecular identification with a representative isolate (KFRIMCC 089) using multigene (ITS, LSU, SSU, TEF1-α, and TUB2) sequence analysis and concatenated phylogenetic analysis (ITS-TEF1-α-TUB2). Pathogenicity tests were also assessed in vitro and in vivo using mycelial disc and spore suspension of L. theobromae, and the isolated fungus's pathogenic behaviour was confirmed after re-isolation and morpho-cultural features. Literature survey reveals that there are no reports of L. theobromae on C. fenestratum from all over the world. Hence, C. fenestratum is being firstly reported as a new host record for L. theobromae from India.

Xylella fastidiosa Outbreak in Israel: Population Genetics, Host Range, and Temporal and Spatial Distribution Analysis

Diseases caused by the insect-transmitted bacterium Xylella fastidiosa have been reported in the Americas since the 19th century, causing diseases such as Pierce's disease of grapevine, almond leaf scorch (ALS), and citrus variegated chlorosis. In the last decade X. fastidiosa was reported from different parts of the world, most notably from southern Italy, infecting olives. In 2017, X. fastidiosa was reported to be associated with ALS symptoms in Israel. Here, we investigated the causal agent of ALS in Israel, its genetic diversity, and host range, and we characterized the temporal and spatial distribution of the disease. X. fastidiosa subsp. fastidiosa sequence type 1 was isolated from symptomatic almond trees and was used to infect almond and grapevine by mechanical inoculation. The pathogen, however, did not infect olive, peach, cherry, plum, nectarine, clementine, and grapefruit plants. Genomic analysis of local isolates revealed that the local population is derived from a single introduction and that they are closely related to X. fastidiosa strains from grapevines in California. Distribution analyses revealed that ALS did not expand from 2017 to 2019; however, since 2020, newly symptomatic trees appeared in the tested orchards. Symptomatic trees were located primarily in clusters, and symptoms tended to spread within rows. Our study confirms that X. fastidiosa is the causal agent of ALS in Israel and describes its genetic and host range characteristics. Although there is no clear evidence yet for the identity of the vectors in Israel, ALS spread continues to threat the almond and grapevine industries in Israel.

Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing

Obtaining complete phytoplasma genomes is difficult due to the lack of a culture system for these bacteria. To improve genome assembly, a non-ionic, low- and iso-osmotic iodixanol (Optiprep™) density gradient centrifugation method was developed to enrich for phytoplasma cells and deplete plant host tissues prior to deoxyribonucleic acid (DNA) extraction and high-throughput sequencing (HTS). After density gradient enrichment, potato infected with a ‘Candidatus Phytoplasma australasia’-related strain showed a ∼14-fold increase in phytoplasma HTS reads, with a ∼1.7-fold decrease in host genomic reads compared to the DNA extracted from the same sample without density gradient centrifugation enrichment. Additionally, phytoplasma genome assemblies from libraries equalized to 5 million reads were, on average, ∼15,000 bp larger and more contiguous (N50 ∼14,800 bp larger) than assemblies from the DNA extracted from the infected potato without enrichment. The method was repeated on capsicum infected with Sweet Potato Little Leaf phytoplasma (‘Ca. Phytoplasma australasia’-related strain) with a lower phytoplasma titer than the potato. In capsicum, ∼threefold more phytoplasma reads and ∼twofold less host genomic reads were obtained, with the genome assembly size and N50 values from libraries equalized to 3.4 million reads ∼137,000 and ∼4,000 bp larger, respectively, compared to the DNA extracted from infected capsicum without enrichment. Phytoplasmas from potato and capsicum were both enriched at a density of 1.049–1.058 g/ml. Finally, we present two highly contiguous ‘Ca. Phytoplasma australasia’ phytoplasma reference genomes sequenced from naturally infected Solanaceae hosts in Australia. Obtaining high-quality phytoplasma genomes from naturally infected hosts will improve insights into phytoplasma taxonomy, which will improve their detection and disease management.

Dominance of Asia II 1 species of Bemisia tabaci in Pakistan and beyond

Globally, Whitefly (Bemisia tabaci) is one of the most important insect pests of crops that causes huge economical losses. The current study was designed to exclusively screen the B. tabaci species in the cotton field of Pakistan during 2017-2020 and have to conduct comparative analysis of B. tabaci species in Asia where Asia II 1 has been reported. A total of 5142 B. tabaci sequences of mitochondrial cytochrome oxidase 1 (mtCO1) from Asian countries were analyzed to determine the species and their distribution in the region. Our analysis over time and space showed that Asia II 1 has gradually dominated over Asia 1 in Punjab Province and over both Asia 1 and MEAM1 in Sindh Province. Asia has been divided into three regions i.e., South Asia (2524 sequences), Southeast Asia (757 sequences) and East Asia (1569 sequences) and dominance of different species of B. tabaci has been determined by calculating the relative percentage of each species. Interestingly, Asia II 1 has been found dominant in the neighboring region (northern zone) of India and also being dominant in its central zone. The dominance of Asia II 1 in Pakistan and northern India explains whitefly epidemic being reported in recent years.

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

Morphological and molecular characterization of Neopestalotiopsis vitis associated with leaf blight disease of Manilkara zapota-a new record from India

Sapota is an important horticultural crop grown in India, and Karnataka is a major producer of sapota. A characteristic leaf blight disease was observed in Southern Karnataka during field surveys conducted in 2019 with an incidence of 13-22% in approximately 45 ha of sapota field. The leaf blight-associated pathogen was isolated on the potato dextrose agar medium. A total of 12 isolates obtained from each location were identified culturally and morphologically. Based on the morphological and cultural features, the pathogen was identified as Pestalotiopsis or Neopestalotiopsis, which was further confirmed by molecular identification using a representative isolate (MZ03). The ITS rDNA and β-tubulin genes were amplified and sequenced using ITS1/ITS4 and T1/T22 primer pairs respectively. nBLAST search analysis and concatenated (ITS-rDNA and TUB2 loci) phylogenetic analysis confirmed the pathogen identity as Neopestalotiopsis vitis. Pathogenicity tests conducted on detached leaves by inoculation with a conidial suspension of N. vitis produced typical blight symptoms after 4-5 days and progressed to cover the entire leaf lamina after 10-12 days. The pathogen's identity was confirmed after re-isolation by cultural and morphological features. Although Pestalotiopsis clavispora and Pestalotiopsis versicolor causing diseases on sapota seedlings and trees have been reported, no reports are available for the occurrence of N. vitis to sapota from India. This is the first report of N. vitis associated with leaf blight disease of sapota from India.

Genome characterization of parsley severe stunt-associated virus in Iran

Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.

Dactuliophora mysorensis sp. nov.: A New Species of Mycelia Sterilia Causing Zonate Leaf Spot on Cowpea in India

Cowpea is an important pulse crop extensively grown in arid and semi-arid tropics which is affected by a number of diseases. Fungi belonging to mycelia sterilia are known to cause many diseases on cereals and pulses. During the cowpea field survey in Mysore District of Karnataka (India), Dactuliophora sp. was identified as the major pathogen causing zonate leaf spot (ZLS) disease. The fungal pathogen was isolated from naturally infected cowpea leaves and identified as a member belongs to the genus Dactuliophora, which was previously described by CLA Leakey in the year 1964 on Vigna unguiculata from Africa. However, detailed morphological and cultural examinations of the pathogen revealed striking differences from that of D. tarrii. Based on differences in morphology with D. tarrii, a new species Dactuliophora mysorensis sp. nov. is described herein. The disease incidence as well as disease index was estimated for 3 years (2016-2018). The severity of the disease was high during August-November. High incidence and disease index of ZLS was recorded in Doddamaragowdanahally region. The pathogenicity tests demonstrated similar symptoms of ZLS. The ITS barcoding revealed that the pathogen is closely related to Rhizoctonia bataticola and Macrophomina phaseolina. Further, in vitro evaluation of fungicides was carried out by poisoned food technique. Among the five fungicides examined, only two systemic fungicides (Benomyl and Carbendazim) were effective against D. mysorensis. Thus, the present study recommends Benomyl and Carbendazim for management of ZLS disease caused by D. mysorensis.

Isolation and characterization of a novel geminivirus from parsley

Fresh leaf vegetables are a significant part of the Persian food. Following a survey for identification of nanoviruses and geminivirus infecting leaf vegetables, a novel geminivirus was identified in a diseased parsley sample showing upward marginal leaf curling, marginal leaf yellowing, dwarfing and reduced leaf size in south-eastern Iran. The genome was identified through combination of rolling circle amplification (RCA) and high throughput sequencing (HTS) approaches. The full-length genome (2779 nts) of the cloned geminivirus, parsley yellow leaf curl virus (PYLCV), shares <66 % genome-wide pairwise identity with all other known geminiviruses. The PYLCV genome has six open reading frames (ORFs) and appears to be a hybrid with the virion sense encoded proteins being most similar to those of becurtoviruses and curtoviruses, whereas the complementary sense encoded proteins are most similar to those of begomoviruses. In comparison with other geminivirus encoded capsid proteins (CPs) and replication associated proteins (Reps), the CP of PYLCV shares <56 % amino acid pairwise identity whereas the Rep shares <73 % amino acid pairwise identity. To demonstrate the pathogenicity of the geminivirus, a partial dimer infectious clone was constructed and used to agro-infect parsley as well as Nicotiana benthamiana, turnip, radish and tomato. The agro-inoculation resulted in infection with symptoms in 83.7 % (82/98) of the tested plant. Based on the similarity of the CP encoded by PYLCV to those of becurtoviruses and curtoviruses, it is likely that leafhoppers may be the primary transmission vector.

Optimized Solid-State Fermentation Medium Enhances the Multienzymes Production from Penicillium citrinum and Aspergillus clavatus

Filamentous fungi play an important role in the production of a range of useful extracellular hydrolytic enzymes for wide industrial applications. The Western Ghats region is known for its rich microbial biodiversity and could be a potential source of several useful fungi that could be exploited for the production of industrially important enzymes. From this soil, we aimed at the isolation of multienzyme producing fungi, optimization of the culture conditions using solid-state fermentation (SSF), partial purification of enzymes and characterization by zymography. Out of seven fungal strains, two isolates, namely Penicillium citrinum and Aspergillus clavatus, were found to produce amylase and cellulase enzymes maximally. The effect of different physicochemical parameters on the production of amylase and cellulase was investigated and the maximum production of multienzymes was achieved in wheat bran substrate. The newly formulated and optimized medium increased the multienzyme production in P. citrinum and A. clavatus as compared to medium with individually optimized parameters. Further, for the first time, different isoforms of amylase and cellulase have been identified from P. citrinum and A. clavatus by zymography. In summary, the present study showed that the filamentous fungi can utilize the industrial waste product such as wheat bran as the substrate for multienzymes production by SSF and could be a promising source of enzymes for biotechnological applications.

Detection of 16SrVI and 16SrIX phytoplasma groups in pot marigold and tickseed plants in northeastern Iran

Pot marigold and tickseed are ornamental plants with many medicinal and cosmetic uses and for landscape, respectively. During a survey in 2018, phyllody symptoms were observed in high percentages in these plants in some regions of the Razavi Khorasan province (northeastern Iran). Total DNA was extracted from symptomatic and asymptomatic plants and polymerase chain reaction was carried on using universal phytoplasma primer pairs P1/P7 and nested primer pairs R16F2n/R16R2. The nested amplification of 1200-bp fragments confirmed the presence of phytoplasmas only in the symptomatic plants. BLAST search, phylogenetic analysis, and virtual RFLP patterns of cloned amplicons allowed to classify the pot marigold phyllody phytoplasma in the 16SrVI-A subgroup while tickseed phyllody was enclosed in the 16SrIX-I subgroup. This is the first report of the association of a 16SrVI phytoplasma with pot marigold phyllody in Iran and of the phytoplasma presence in tickseed.

A new collar rot disease of cowpea (Vigna unguiculata) caused by Aplosporella hesperidica in India

Cowpea is an important pulse crop cultivated in arid and semi-arid regions of the world. During field survey, a characteristic wilt was observed in around 45 ha of cowpea fields with incidence 17-25%. Infection was seen in pre-flowering stage and infected plants showed quick wilt symptoms with tan lesions near the stem-soil interface. Fungal pathogens associated were isolated on PDA, which produced dark to grey olivaceous colonies in the centre, and aerial mycelia were appressed with floccose and white to smoke-grey. Conidia are aseptate, initially hyaline, smooth-walled, broadly ellipsoidal with rounded ends becoming dark brown. Based on these morphological features, the fungal pathogen was identified as Aplosporella sp. The ITS-rDNA region was amplified using ITS1/ITS4 primers and sequenced. The nBLAST and phylogenetic analysis confirmed the pathogen as Aplosporella hesperidica. The Koch's postulates were performed on 45-days-old cowpea plants with mycelial disc of A. hesperidica. Development of typical necrotic lesions was observed after 28 days of post-inoculation and the pathogen's identity was confirmed based on re-isolation. Efficacy of fungicides evaluated in vitro showed that the pathogen is highly sensitive to systemic fungicides rather than the contact fungicides. The cowpea production was severely affected owing to the causative agent A. hesperidica. The collar rot disease of cowpea by A. hesperidica is the first report in India. SIGNIFICANCE AND IMPACT OF THE STUDY: A new collar rot disease of cowpea recorded from India has been investigated. The necrotic lesions were enlarged and eventually quick wilt and death of the host plant was observed with incidence ranged from 17 to 25%. Associated fungal pathogen was isolated and identified as Aplosporella hesperidica based on morphology and ITS-rDNA sequence analysis. Koch's postulates were performed under greenhouse conditions and in vitro evaluation of fungicides shows that the pathogen is sensitive to systemic fungicides. This is the first report of A. hesperidica causing collar rot disease of cowpea in India.

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host-pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited. In this work, we have obtained an RNA-seq-based differential expression profile of Mexican lime plants challenged against CLas infection, at both asymptomatic and symptomatic stages. Typical HLB-responsive differentially expressed genes (DEGs) are involved in photosynthesis, secondary metabolism, and phytohormone homeostasis. Enrichment of DEGs associated with biotic response showed that genes related to cell wall, secondary metabolism, transcription factors, signaling, and redox reactions could play a role in the tolerance of Mexican lime against CLas infection. Interestingly, despite some concordance observed between transcriptional responses of different tolerant citrus species, a subset of DEGs appeared to be species-specific. Our data highlights the importance of studying the host response during HLB disease using as model tolerant citrus species, in order to design new and opportune diagnostic and management methods.

Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II-Bemisia tabaci mitotypes in Pakistan

Endosymbionts associated with the whitefly Bemisia tabaci cryptic species are known to contribute to host fitness and environmental adaptation. The genetic diversity and population complexity were investigated for endosymbiont communities of B. tabaci occupying different micro-environments in Pakistan. Mitotypes of B. tabaci were identified by comparative sequence analysis of the mitochondria cytochrome oxidase I (mtCOI) gene sequence. Whitefly mitotypes belonged to the Asia II-1, -5, and -7 mitotypes of the Asia II major clade. The whitefly-endosymbiont communities were characterized based on 16S ribosomal RNA operational taxonomic unit (OTU) assignments, resulting in 43 OTUs. Most of the OTUs occurred in the Asia II-1 and II-7 mitotypes (r 2 = .9, p < .005), while the Asia II-5 microbiome was less complex. The microbiome OTU groups were mitotype-specific, clustering with a basis in phylogeographical distribution and the corresponding ecological niche of their whitefly host, suggesting mitotype-microbiome co-adaptation. The primary endosymbiont Portiera was represented by a single, highly homologous OTU (0%-0.67% divergence). Two of six Arsenophonus OTUs were uniquely associated with Asia II-5 and -7, and one occurred exclusively in Asia II-1, two only in Asia II-5, and one in both Asia II-1 and -7. Four other secondary endosymbionts, Cardinium, Hemipteriphilus, Rickettsia, and Wolbachia OTUs, were found at ≤29% frequencies. The most prevalent Arsenophonus OTU was found in all three Asia II mitotypes (55% frequency), whereas the same strain of Cardinium and Wolbachia was found in both Asia II-1 and -5, and a single Hemipteriphilus OTU occurred in Asia II-1 and -7. This pattern is indicative of horizontal transfer, suggestive of a proximity between mitotypes sufficient for gene flow at overlapping mitotype ecological niches.

De novo assembly and functional annotation of Citrus aurantifolia transcriptome from Candidatus Liberibacter asiaticus infected and non-infected trees

Mexican lime (Citrus aurantifolia) belongs to the Rutaceae family and nowadays is one of the major commercial citrus crops in different countries. In Mexico, Mexican lime production is impaired by Huanglongbing (HLB) disease associated to Candidatus Liberibacter asiaticus (CLas) bacteria. To date, transcriptomic studies of CLas-Citrus interaction, have been performed mainly in sweet citrus models at symptomatic (early) stage where pleiotropic responses could mask important, pathogen-driven host modulation as well as, host antibacterial responses. Additionally, well-assembled reference transcriptomes for acid limes including C. aurantifolia are not available. The development of improved transcriptomic resources for CLas-citrus pathosystem, including both asymptomatic (early) and symptomatic (late) stages, could accelerate the understanding of the disease. Here, we provide the first transcriptomic analysis from healthy and HLB-infected C. aurantifolia leaves at both asymptomatic and symptomatic stages, using a RNA-seq approach in the Illumina NexSeq500 platform. The construction of the assembled transcriptome was conducted using the predesigned workflow Transflow and a total of 41,522 tentative transcripts (TTs) obtained. These C. aurantifolia TTs were functionally annotated using TAIR10 and UniProtKB databases. All raw reads were deposited in the NCBI SRA with accession numbers SRR10353556, SRR10353558, SRR10353560 and SRR10353562. Overall, this dataset adds new transcriptomic valuable tools for future breeding programs, will allow the design of novel diagnostic molecular markers, and will be an essential tool for studying the HLB disease.

Opuntin B, the antiviral protein isolated from prickly pear (Opuntia ficus-indica (L.) Miller) cladode exhibits ribonuclease activity

An antiviral protein, designated Opuntin B, was purified from Prickly Pear (Opuntia ficus-indica (L.) Miller) Cladode by heat treatment of the extract, protein precipitation by ammonium sulfate treatment followed by ion-exchange chromatography. Assessment of enzymatic activity of the purified protein showed that it degrades total plant genomic RNA, while causing electrophoretic mobility shifting of Cucumber mosaic virus (CMV) RNAs. However, heat-denatured viral RNA became sensitive to degradation upon treatment with antiviral protein. Opuntin B had no DNase activity on native and heat-denatured apricot genomic DNA, and on PCR-amplified coat protein gene of CMV. Using CMV as prey protein and Opuntin B as bait protein, no interaction was found between the antiviral protein and viral coat protein in far western dot blot analysis.

Identification of the wild and cultivated hosts of wheat dwarf virus and oat dwarf virus in Iran

In the last decade two mastreviruses, Wheat dwarf virus (WDV) and Oat dwarf virus (ODV) have been reported from cereal farms in Iran. In a survey, wild and cultivated hosts of these mastreviruses were studied during 2015 to 2017. Symptomatic small grain cereal samples and weed species were collected and assayed for WDV and/or ODV infection by PCR. While WDV which was detected in 139/284 (49%) of total symptomatic samples, low incidence (2%) was recorded for ODV which was detected only in slender wild oat (Avena barbata Pott ex Link) and red brome (Bromus rubens L.). In agroinfection studies, the clone of ODV infected common oat (A. sativa) and slender wild oat (A. barbata) with the low efficiency and did not infect wheat or barley. ODV was transmitted by the leafhopper Psammotettix alienus, from agroinfected common oat to healthy seedlings. The results show that, in contrast to WDV, ODV has a low incidence and a narrow host range in gramineous plants.

Novel nanovirus and associated alphasatellites identified in milk vetch plants with chlorotic dwarf disease in Iran

Members of the family Nanoviridae are multi-component single-stranded DNA viruses that infect a variety of plant species. Using a combination of conventional PCR and high throughput sequencing-based approach, we identified a novel nanovirus infecting two symptomatic milk vetch plants (Astragalus myriacanthus Boiss.; family Fabaceae) showing marginal leaf chlorosis, little leaves and dwarfing in Iran. All eight segments (DNA-C, DNA-M, DNA-N, DNA-R, DNA-S, DNA-U1, DNA-U2 and DNAU4) were recovered and Sanger sequenced. The genome of this new nanovirus, hereby referred to as milk vetch chlorotic dwarf virus (MVCDV), shares 62.2-74.7 % nucleotide pairwise identity with the genomes of other nanoviruses. DNA-C, DNA-M, DNA-N, DNA-S components are most closely related to those of black medic leaf roll virus (BMLRV), sharing between 67.8-81.2 % identity. We also identified three nanoalphasatellites (family Alphasatellitidae) associated with the nanovirus which belong to species Faba bean necrotic yellows alphasatellite 1 (genus Subclovsatellite), Faba bean necrotic yellows alphasatellite 2 (genus Fabenesatellite) and Sophora yellow stunt alphasatellite 5 (genus Clostunsatellite). Given the significant diversity of Astragalus spp. in Iran, it is likely that there could be more nanoviruses circulating in these plants and that these may play a role in the spread of these nanovirus to cultivated fabaceous hosts.

Amorphophallus konjac anthracnose caused by Colletotrichum siamense in China

AIMS

Amorphophallus konjac is an important commercial crop grown in China because it is the only plant species which is rich in glucomannan concentration. Recently, an outbreak of anthracnose (incidence ranging from 10-15%) was observed in a field survey conducted from June to August 2018. This study aims to identify the causal agent of A. konjac anthracnose.

METHODS AND RESULTS

The pathogen was isolated on potato dextrose agar (PDA) medium. The fungal colony on PDA was greyish to dark grey. Conidia were falcate, one-celled and hyaline. Based on the micro-morphological and cultural characteristics, the pathogen was identified as Colletotrichum sp. blast search and phylogenetic analysis of the ITS, GAPDH, CHS1, ACT, CAL and TUB2 genes revealed the pathogen as Colletotrichum siamense. Koch's postulates were conducted on 2-month konjac leaves with conidial suspension. Development of typical anthracnose disease was recorded 5 days after inoculation and the pathogen's identity was confirmed by re-isolation and molecular identification.

CONCLUSIONS

Amorphophallus konjac anthracnose was caused by C. siamense in China.

SIGNIFICANCE AND IMPACT OF THE STUDY

Identification of causal agent of A. konjac anthracnose will be helpful in designing effective disease control strategies.

Immunological detection of the Weligama coconut leaf wilt disease associated phytoplasma: Development and validation of a polyclonal antibody based indirect ELISA

Weligama coconut leaf wilt disease (WCLWD) causes heavy losses in the coconut cultivations of southern Sri Lanka. The in-house developed and validated indirect ELISA was based on specific polyclonal antibodies raised in female New Zealand White rabbits, against partially purified WCLWD associated phytoplasma. This ELISA has the potential to distinguish secA PCR confirmed, WCLWD associated phytoplasma positive palms from phytoplasma free palms at high accuracy (93%) and sensitivity (92.7%), but with marginal specificity (79%). The calculated ELISA cross reactivity index (CRI) values were low for sugarcane white leaf (7%) and sugarcane grassy shoot (8%) infected leaves, but with marked highCRIfor both Bermuda grass white leaf (69%) and areca nut yellow leaf (70%) infected leaves. SecA gene based phylogenetic relationships of the WCLWD associated phytoplasma with these other locally prevalent phytoplasma strains elucidated this immunological cross reactivity, which was further reiterated by virtual restriction fragment length polymorphism analysis. Based on scanning electron microscopy, this study provides additional visual evidence, for the presence of phytoplasmas in WCLWD infected tissues.

Association of a 'Candidatus Phytoplasma aurantifolia'-related strain with apricot showing European stone fruit yellows symptoms in Iran

During 2012-2015 surveys in some orchards in Faraghe (Iran), a number of apricot trees showed symptoms resembling those associated with the phytoplasma disease known as European stone fruit yellows that are severe leaf roll, yellowing and die back. The presence of an infectious agent was confirmed by graft transmission experiments in which all the previously symptomless GF-677 (peach × almond) trees showed phytoplasma-type symptoms. The phytoplasma presence was confirmed by nested PCR assays using DNA extracted from samples from both field collected and graft-inoculated trees. The sequences of four nested PCR products from symptomatic apricot and experimentally graft-inoculated GF-677 trees were 100% identical to each other. RFLP and phylogenetic analyses carried out on these sequences allowed to cluster the strain infecting apricot trees in Iran with the16SrII-C subgroup phytoplasmas. This is the first report of a 16SrII-C phytoplasma associated with leaf roll and yellowing of the leaves in apricot trees.

Presence of chelonid herpesvirus 5 (ChHV5) in sea turtles in northern Sinaloa, Mexico

The presence of fibropapilloma and its associated chelonid herpesvirus 5 (ChHV5) was assessed in 82 wild sea turtles. Olive ridley turtles Lepidochelys olivacea (n = 58) were caught in the pelagic Area of Marine Influence (AMI) (off the coast of Guasave, Sinaloa), and black turtles Chelonia mydas agassizii (n = 24) were captured in the Navachiste Lagoon System. The apparent physical condition was evaluated as 'good' or 'poor' by physical examination. The population structure and general health status was determined by condition index, hematocrit and total plasma protein. Detection of ChHV5 from skin samples was done by PCR. The overall physical condition of black turtles was good and all the individuals were tumor-free. Likewise, the physical condition of most olive ridley turtles was good, except for 10 individuals with poor condition. Of these, 4 had fibropapilloma-like tumors. PCR analyses showed that 3 tumors were ChHV5-positive. The DNA sequence showed 96% identity with ChHV5. All other skin samples from black or olive ridley turtles were ChHV5-negative. This is the first report of fibropapillomatosis-ChHV5 in foraging grounds off northern Sinaloa. The virus was present in a small proportion of L. olivacea individuals, a free-ranging species. It is suggested that infected turtles acquired the virus at a different location somewhere during their development before arriving in the AMI zone. This finding makes the case for setting up a health monitoring program for turtle populations in the area, enforcing sanitary measures to reduce the spread of the pathogen.

Pathogen Risk Analysis for Wild Amphibian Populations Following the First Report of a Ranavirus Outbreak in Farmed American Bullfrogs (Lithobates catesbeianus) from Northern Mexico

Ranaviruses are the second deadliest pathogens for amphibian populations throughout the world. Despite their wide distribution in America, these viruses have never been reported in Mexico, the country with the fifth highest amphibian diversity in the world. This paper is the first to address an outbreak of ranavirus in captive American bullfrogs (Lithobates catesbeianus) from Sinaloa, Mexico. The farm experienced high mortality in an undetermined number of juveniles and sub-adult bullfrogs. Affected animals displayed clinical signs and gross lesions such as lethargy, edema, skin ulcers, and hemorrhages consistent with ranavirus infection. The main microscopic lesions included mild renal tubular necrosis and moderate congestion in several organs. Immunohistochemical analyses revealed scant infected hepatocytes and renal tubular epithelial cells. Phylogenetic analysis of five partial ranavirus genes showed that the causative agent clustered within the Frog virus 3 clade. Risk assessment with the Pandora⁺ protocol demonstrated a high risk for the pathogen to affect amphibians from neighboring regions (overall Pandora risk score: 0.619). Given the risk of American bullfrogs escaping and spreading the disease to wild amphibians, efforts should focus on implementing effective containment strategies and surveillance programs for ranavirus at facilities undertaking intensive farming of amphibians.

The Relative Occurrence of Grapevine leafroll-associated virus 3 and Grapevine red blotch virus in Washington State Vineyards

Vineyard surveys were conducted for three consecutive seasons in eastern Washington State, the major grapevine-growing region in the state, to document the occurrence of Grapevine leafroll-associated virus 3 (GLRaV-3) and Grapevine red blotch virus (GRBV). The majority of samples were collected from red-berried wine grape (Vitis vinifera) cultivars exhibiting symptoms of or suspected for grapevine leafroll (GLD) and red blotch (GRBD) diseases. A limited number of samples from white-berried cultivars were collected randomly due to the lack of visual symptoms. Samples were collected from a total of 2,063 grapevines from 18 red-berried cultivars and seven white-berried cultivars planted in eight American Viticultural Areas and tested for GLRaV-3 and GRBV using RT-PCR and PCR, respectively. The results showed 67.77% and 6.01% of total samples positive for GLRaV-3 and GRBV, respectively, and 9.06% of samples positive for both viruses. About 17% of samples tested negative for the two viruses, but some of these samples were positive for GLRaV-2 and GLRaV-4. Overall results indicated that GLRaV-3 was more common than GRBV, independent of cultivars and the geographic origin of samples. Due to variability in symptoms in red-berried cultivars, virus-specific diagnostic assays were deemed necessary for reliable identification of GLRaV-3 and GRBV and to differentiate GLD and GRBD symptoms from those induced by biotic and abiotic stresses in vineyards. A multiplex PCR protocol was developed for simultaneous detection of GLRaV-3 and GRBV in grapevine samples. A global phylogenetic analysis of GRBV genome sequences revealed segregation of virus isolates from Washington State vineyards into two distinct clades, with the majority of isolates belonging to clade II.

Comparison of Different Procedures for DNA Extraction for Routine Diagnosis of Phytoplasmas

This chapter presents five different procedures for extracting DNA from phytoplasma-infected plants and insect vectors suitable for PCR assays. One of these procedures enriches phytoplasma DNA through differential centrifugation and is effective in producing highly purified DNA from fresh tissues from a wide variety of herbaceous and woody plants. Although the DNA yield is less than those of other known total DNA extraction procedures, a major advantage of the presented phytoplasma-enriched procedure is that a substantial proportion of the isolated DNA is from phytoplasmas. The other four procedures here presented involve treatments with CTAB-based buffer to lyse cells and purify DNA followed by deproteination and recovery of DNA. These procedures work well for extracting total DNA from fresh, frozen, or lyophilized tissues from a wide variety of plant hosts as well as insect vectors. Because few manipulations are required, the CTAB-based procedures are faster and easier to perform than the phytoplasma-enrichment protocol. In addition, they result in very high yields and provide DNA that is less pure but of suitable quality for the use in standard molecular biological techniques including PCR assays.

Survival and development of potato psyllid (Hemiptera: Triozidae) on Convolvulaceae: Effects of a plant-fungus symbiosis (Periglandula)

Plant species in the family Solanaceae are the usual hosts of potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Psylloidea: Triozidae). However, the psyllid has also been shown to develop on some species of Convolvulaceae (bindweeds and morning glories). Developmental success on Convolvulaceae is surprising given the rarity of psyllid species worldwide associated with this plant family. We assayed 14 species of Convolvulaceae across four genera (Convolvulus, Calystegia, Ipomoea, Turbina) to identify species that allow development of potato psyllid. Two populations of psyllids were assayed (Texas, Washington). The Texas population overlaps extensively with native Convolvulaceae, whereas Washington State is noticeably lacking in Convolvulaceae. Results of assays were overlain on a phylogenetic analysis of plant species to examine whether Convolvulaceae distantly related to the typical host (potato) were less likely to allow development than species of Convolvulaceae more closely related. Survival was independent of psyllid population and location of the plant species on our phylogenetic tree. We then examined whether presence of a fungal symbiont of Convolvulaceae (Periglandula spp.) affected psyllid survival. These fungi associate with Convolvulaceae and produce a class of mycotoxins (ergot alkaloids) that may confer protection against plant-feeding arthropods. Periglandula was found in 11 of our 14 species, including in two genera (Convolvulus, Calystegia) not previously known to host the symbiont. Of these 11 species, leaf tissues from five contained large quantities of two classes of ergot alkaloids (clavines, amides of lysergic acid) when evaluated by LC-MS/MS. All five species also harbored Periglandula. No ergot alkaloids were detected in species free of the fungal symbiont. Potato psyllid rapidly died on the five species that harbored Periglandula and contained ergot alkaloids, but survived to adulthood on seven of the nine species in which ergot alkaloids were not detected. These results support the hypothesis that a plant-fungus symbiotic relationship affects the suitability of certain Convolvulaceae to potato psyllid.

'Candidatus Liberibacter solanacearum' Is Tightly Associated with Carrot Yellows Symptoms in Israel and Transmitted by the Prevalent Psyllid Vector Bactericera trigonica

Carrot yellows disease has been associated for many years with the Gram-positive, insect-vectored bacteria, 'Candidatus Phytoplasma' and Spiroplasma citri. However, reports in the last decade also link carrot yellows symptoms with a different, Gram-negative, insect-vectored bacterium, 'Ca. Liberibacter solanacearum'. Our study shows that to date 'Ca. L. solanacearum' is tightly associated with carrot yellows symptoms across Israel. The genetic variant found in Israel is most similar to haplotype D, found around the Mediterranean Basin. We further show that the psyllid vector of 'Ca. L. solanacearum', Bactericera trigonica, is highly abundant in Israel and is an efficient vector for this pathogen. A survey conducted comparing conventional and organic carrot fields showed a marked reduction in psyllid numbers and disease incidence in the field practicing chemical control. Fluorescent in situ hybridization and scanning electron microscopy analyses further support the association of 'Ca. L. solanacearum' with disease symptoms and show that the pathogen is located in phloem sieve elements. Seed transmission experiments revealed that while approximately 30% of the tested carrot seed lots are positive for 'Ca. L. solanacearum', disease transmission was not observed. Possible scenarios that may have led to the change in association of the disease etiological agent with carrot yellows are discussed. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Characterization of a 16SrII subgroup D phytoplasma strain associated with Calendula officinalis phyllody in Iran

Calendula officinalis plants with phyllody symptoms (CaoP) were observed in Yazd and Ashkezar (Yazd province, Iran) during 2013-2016. Twenty-one symptomatic and four asymptomatic plants were transferred individually to the greenhouse and potted for the biological and molecular characterization of associated phytoplasma. The dodder transmission from symptomatic potted marigold plants, induced virescence, phyllody and witches' broom symptoms in periwinkle. Total DNAs extracted from symptomatic and symptomless plants and dodder-inoculated periwinkles were subjected to nested PCR assay using primer pairs amplifying phytoplasma ribosomal DNA. Expected PCR amplification was detected in all CaoP plant and dodder-inoculated periwinkle samples. RFLP analysis of the amplicons obtained in direct PCR with P1/P7 primers using RsaI, AluI, MseI, HinfI and HaeIII restriction enzymes showed profiles identical to each other and related to phytoplasmas in all the 21 positive samples. R16mF2/R16mR2 amplicons from six CaoP plant samples were sequenced where consensus sequences had 100% of identity among each other. R16F2n/R16R2-trimmed sequences (1248 bp) of representative samples from Yazd and Ashkezar were deposited in GenBank under accession numbers KU297202 and MH065715, respectively. BLAST search and phylogenetic analysis showed that the CaoP phytoplasma had 99% homology and clusters with phytoplasmas in group 16SrII. Computer-simulated analysis using iPhyClassifier suggests that the CaoP RFLP 16S rRNA gene pattern was identical to 16SrII-D phytoplasmas subgroup. Phytoplasma strains (16SrII-D) were reported as alfalfa witches' broom disease agent previously in the same geographic areas, and it is possible that alfalfa plays a role in the epidemiology of CaoP disease or vice-versa.

Establishment of an efficient genetic transformation method in Dunaliella tertiolecta mediated by Agrobacterium tumefaciens

Microalgae are photosynthetic microorganisms widely used for the production of highly valued compounds, and recently they have been shown to be promising as a system for the heterologous expression of proteins. Several transformation methods have been successfully developed, from which the Agrobacterium tumefaciens-mediated method remains the most promising. However, microalgae transformation efficiency by A. tumefaciens is shown to vary depending on several transformation conditions. The present study aimed to establish an efficient genetic transformation system in the green microalgae Dunaliella tertiolecta using the A. tumefaciens method. The parameters assessed were the infection medium, the concentration of the A. tumefaciens and co-culture time. As a preliminary screening, the expression of the gusA gene and the viability of transformed cells were evaluated and used to calculate a novel parameter called Transformation Efficiency Index (TEI). The statistical analysis of TEI values showed five treatments with the highest gusA gene expression. To ensure stable transformation, transformed colonies were cultured on selective medium using hygromycin B and the DNA of resistant colonies were extracted after five subcultures and molecularly analyzed by PCR. Results revealed that treatments which use solid infection medium, A. tumefaciens OD₆₀₀ = 0.5 and co-culture times of 72 h exhibited the highest percentage of stable gusA expression. Overall, this study established an efficient, optimized A. tumefaciens-mediated genetic transformation of D. tertiolecta, which represents a relatively easy procedure with no expensive equipment required. This simple and efficient protocol opens the possibility for further genetic manipulation of this commercially-important microalgae for biotechnological applications.

Nucleic acid purification from plants, animals and microbes in under 30 seconds

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.

CRISPR/Cas9 Editing of the Codling Moth (Lepidoptera: Tortricidae) CpomOR1 Gene Affects Egg Production and Viability

The codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is a major pest of pome fruit worldwide. Incorporation of semiochemicals, including the main sex pheromone (codlemone), into codling moth IPM programs has drastically reduced the amount of chemical insecticides needed to control this orchard pest. Odorant receptors located in sensory neuron membranes in the antennae are key sensors in the detection of semiochemicals and trigger downstream signaling events leading to a behavioral response. CpomOR1 is an odorant receptor belonging to the pheromone receptor subfamily in codling moth, and is a prime candidate for being a codlemone receptor based on its high expression levels in male antennae. In this study, the CpomOR1 gene was targeted using CRISPR/Cas9 genome editing to knockdown functional OR1 protein production to determine physiological function(s). By injecting early stage eggs, mutations were successfully introduced, including both deletions and insertions. When attempting to create stable populations of codling moth through mating of males with females containing mutations of the CpomOR1 gene, it was found that fecundity and fertility were affected, with edited females producing nonviable eggs. The role of CpomOR1 in fecundity and fertility in codling moth is unknown and will be the focus of future studies.

Identification of a Nanovirus-Alphasatellite Complex in Sophora alopecuroides

Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had similarities to nanovirus genome components. From this plant, the nanovirus-like molecules DNA-R (n=4), DNA-C (n=2), DNA-S (n=1), DNA-M (n=1), DNA-N (n=1), DNA-U1 (n=1), DNA-U2 (n=1) and DNA-U4 (n=1) were amplified, cloned and sequenced. Other than for the DNA-R, these components share less than 71% identity with those of other known nanoviruses. The four DNA-R molecules were highly diverse, sharing only 65-71% identity with each other and 64-86% identity with those of other nanoviruses. In the S. alopecuroides plant 14 molecules sharing 57.7-84.6% identity with previously determined sequences of nanovirus-associated alphasatellites were also identified. Given the research activity in the nanovirus field during the last five years coupled with high-throughput sequence technologies, many more diverse nanoviruses and nanovirus-associated satellites are likely to be identified.

Bacterial Endosymbionts of the Psyllid Cacopsylla pyricola (Hemiptera: Psyllidae) in the Pacific Northwestern United States

Insects often have facultative associations with bacterial endosymbionts, which can alter the insects' susceptibility to parasitism, pathogens, plant defenses, and certain classes of insecticides. We collected pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae), from pear orchards in Washington and Oregon, and surveyed them for the presence of bacterial endosymbionts. Adult psyllids were collected on multiple dates to allow us to assay specimens of both the summer ("summerform") and the overwintering ("winterform") morphotypes. Two endosymbionts, Arsenophonus and Phytoplasma pyri, were detected in psyllids of both morphotypes in both states. A separate survey revealed similar associations present in psyllids collected in 1987. Arsenophonus was present in 80-100% of psyllids in all growing regions. A slightly lower proportion of summerform than winterform psyllids harbored the bacterium. Arsenophonus was present in the bacteriomes and developing oocytes of most psyllids, indicating that this endosymbiont is transovarially transmitted. This bacterium was also observed in the salivary glands and midguts of some psyllids. Phytoplasma pyri was present in a greater proportion of pear psylla from orchards near Yakima, WA, than from other regions, and was present in a higher proportion of winterforms than summerforms. We did not detect Wolbachia, Profftella, or Liberibacter europaeus, which are associated with other psyllid pests, including other species of Cacopsylla. Our study is the first to survey North American populations of C. pyricola for endosymbionts, and provides a foundation for further research on how bacterial associations may influence the ecology and management of this pest.

"Candidatus Liberibacter solanacearum" Associated With the Psyllid, Bactericera maculipennis (Hemiptera: Triozidae)

The psyllid Bactericera maculipennis (Crawford) (Hemiptera: Triozidae) often cohabits field bindweed (Convolvulus arvensis, Solanales: Convolvulaceae) and other plants with the congeneric psyllid, Bactericera cockerelli (Šulc), in the Pacific Northwestern United States. Bactericera cockerelli is a vector of "Candidatus Liberibacter solanacearum," the pathogen associated with zebra chip disease of potato (Solanales: Solanaceae). Because B. maculipennis and B. cockerelli both naturally occur on certain plants, we surveyed B. maculipennis adults collected from Washington and Idaho for presence of "Ca. L. solanacearum" to determine whether this psyllid also harbors this pathogen. Liberibacter was present in 30% of field-collected B. maculipennis and in 100% of colony-reared psyllids. Sequences of 16S rDNA and microsatellite markers revealed that "Ca. L. solanacearum" from B. maculipennis was closely related to Liberibacter haplotype B from B. cockerelli. Results of laboratory assays demonstrated that Liberibacter can be transmitted between B. cockerelli and B. maculipennis on plants within the Convolvulaceae. Potato plants challenged with Liberibacter-infected B. maculipennis did not become infected, apparently because potato is not a suitable host for the psyllid. We therefore conclude that B. maculipennis is not a direct threat to potato production, despite its association with Liberibacter. We are the first to report that "Ca. L. solanacearum" is associated with a psyllid other than B. cockerelli in North America. Results of our study demonstrate the importance of understanding the complete ecology of psyllids-including interactions with other psyllids on non-crop hosts-in predicting what crops or regions are potentially susceptible to the spread of Liberibacter.

Stubborn Disease in Iran: Diversity of Spiroplasma citri Strains in Circulifer haematoceps Leafhoppers Collected in Sesame Fields in Fars Province

Spiroplasma citri is a bacterial pathogen responsible for the economically important citrus stubborn disease. Sesame and citrus seeds serve as hosts for both S. citri and its leafhopper vector Circulifer haematoceps. To evaluate whether sesame could act as a reservoir for citrus-infecting strains or not, the genetic diversity among S. citri strains found in leafhoppers collected in citrus and citrus-free sesame fields was investigated. Among 26 periwinkle plants exposed to the collected C. haematoceps leafhoppers, 12 plants developed typical stubborn symptoms. All symptomatic periwinkles were polymerase chain reaction positive using S. citri-specific primer pairs targeting the spiralin and P89 genes. Phylogenetic trees based on spiralin gene sequence analysis indicated that the novel field-collected strains clustered with those belonging to two formerly defined S. citri groups (groups 6 and 1). In addition, our results strongly suggest that group 1 strains could be transmitted from sesame-infected plants to citrus trees by C. haematoceps, while group 6 strains may not infect citrus trees.

Splicing features in the expression of the complementary-sense genes of Beet curly top Iran virus

Beet curly top Iran virus (BCTIV) is a distinct geminivirus which has been reported from sugar-beet-growing farms in Iran. In this study, the role of the splicing in expression of complementary-sense genes of BCTIV was studied. Total RNA was extracted from BCTIV-infected tissue, and the predicted intron position of complementary-sense mRNA transcripts was amplified by RT-PCR followed by cloning of the amplicons. Sequence confirmed that both spliced and unspliced mRNAs are synthesized by the same transcription unit. Sequence comparison showed that a 155-nt segment (intron) corresponding to nucleotides 1890-2044 of the viral genome has been removed from the latter transcript and therefore fusion of the C1:C2 genes resulted creation of a continuous reading frame for potential production of intact replication initiator protein (Rep). BCTIV intron comprises of most consensus splicing signals required for splicing in eukaryotes and several plant viruses including mastre- and capulaviruses.

Genetic diversity and vector transmission of phytoplasmas associated with sesame phyllody in Iran

During 2010-14 surveys in the major sesame growing areas of Fars, Yazd and Isfahan provinces (Iran), genetic diversity and vector transmission of phytoplasmas associated with sesame phyllody were studied. Virtual RFLP, phylogenetic, and DNA homology analyses of partial 16S ribosomal sequences of phytoplasma strains associated with symptomatic plants revealed the presence of phytoplasmas referable to three ribosomal subgroups, 16SrII-D, 16SrVI-A, and 16SrIX-C. The same analyses using 16S rDNA sequences from sesame phyllody-associated phytoplasmas retrieved from GenBank database showed the presence of phytoplasmas clustering with strains in the same subgroups in other Iranian provinces including Bushehr and Khorasan Razavi. Circulifer haematoceps and Orosius albicinctus, known vectors of the disease in Iran, were tested for transmission of the strains identified in this study. C. haematoceps transmitted 16SrII-D, 16SrVI-A, and 16SrIX-C phytoplasmas, while O. albicinctus only transmitted 16SrII-D strains. Based on the results of the present study and considering the reported presence of phytoplasmas belonging to the same ribosomal subgroups in other crops, sesame fields probably play an important role in the epidemiology of other diseases associated with these phytoplasmas in Iran.

Assessing the Likelihood of Transmission of Candidatus Liberibacter solanacearum to Carrot by Potato Psyllid, Bactericera cockerelli (Hemiptera: Triozidae)

'Candidatus Liberibacter solanacearum' (Lso) is a phloem-limited bacterium that severely affects important Solanaceae and Apiaceae crops, including potato, tomato, pepper, tobacco, carrot and celery. This bacterium is transmitted to solanaceous species by potato psyllid, Bactericera cockerelli, and to Apiaceae by carrot psyllids, including Trioza apicalis and Bactericera trigonica. Five haplotypes of Lso have so far been described, two are associated with solanaceous species and potato psyllids, whereas the other three are associated with carrot and celery crops and carrot psyllids. Little is known about cross-transmission of Lso to carrot by potato psyllids or to potato by carrot psyllids. Thus, the present study assessed whether potato psyllid can transmit Lso to carrot and whether Lso haplotypes infecting solanaceous species can also infect carrot and lead to disease symptom development. In addition, the stylet probing behavior of potato psyllid on carrot was assessed using electropenetrography (EPG) technology to further elucidate potential Lso transmission to Apiaceae by this potato insect pest. Results showed that, while potato psyllids survived on carrot for several weeks when confined on the plants under controlled laboratory and field conditions, the insects generally failed to infect carrot plants with Lso. Only three of the 200 carrot plants assayed became infected with Lso and developed characteristic disease symptoms. Lso infection in the symptomatic carrot plants was confirmed by polymerase chain reaction assay and Lso in the carrots was determined to be of the haplotype B, which is associated with solanaceous species. EPG results further revealed that potato psyllids readily feed on carrot xylem but rarely probe into the phloem tissue, explaining why little to no Lso infection occurred during the controlled laboratory and field cage transmission trials. Results of our laboratory and field transmission studies, combined with our EPG results, suggest that the risk of Lso infection and spread between psyllid-infested solanaceous and Apiaceae crops is likely to be negligible under normal field conditions.

Gut Content Analysis of a Phloem-Feeding Insect, Bactericera cockerelli (Hemiptera: Triozidae)

Potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae), is a key pest of potato (Solanum tuberosum L., Solanales: Solanaceae) and a vector of "Candidatus Liberibacter solanacearum," the pathogen associated with zebra chip disease. In addition to its presence on cultivated crops, the psyllid regularly occurs on numerous uncultivated annual and perennial species within the Solanaceae. A better understanding of landscape-level ecology of B. cockerelli would substantially improve our ability to predict which potato fields are most likely to be colonized by infected psyllids. We developed three PCR-based methods of gut content analysis to identify what plant species B. cockerelli had previously fed upon. These methods included-1) sequencing PCR amplicons of regions of plant-derived internal transcribed spacer (ITS) or the chloroplast trnL gene from psyllids, 2) high-resolution melting analysis of ITS or trnL real-time PCR products, and 3) restriction enzyme digestion of trnL PCR product. Each method was used to test whether we could identify psyllids that had been reared continuously on potato versus psyllids reared continuously on the perennial nightshade, Solanum dulcamara. All three methods of gut content analysis correctly identified psyllids from potato and psyllids from S. dulcamara Our study is the first to demonstrate that plant DNA can be detected in a phloem-feeding insect. Gut content analysis, in combination with other landscape ecology approaches, could help elucidate patterns in landscape-level movements and host plant associations of B. cockerelli.