Chlorotic Fleck Research Articles

A new and effective method to induce infection of Phyllachora maydis into corn for tar spot studies in controlled environments

BackgroundTar spot of corn is a significant and spreading disease in the continental U.S. and Canada caused by the obligate biotrophic fungus Phyllachora maydis. As of 2023, tar spot had been reported in 18 U.S. states and one Canadian Province. The symptoms of tar spot include chlorotic flecking followed by the formation of black stromata where conidia and ascospores are produced. Advancements in research and management for tar spot have been limited by a need for a reliable method to inoculate plants to enable the study of the disease. The goal of this study was to develop a reliable method to induce tar spot in controlled conditions.ResultsWe induced infection of corn by P. maydis in 100% of inoculated plants with a new inoculation method. This method includes the use of vacuum-collection tools to extract ascospores from field-infected corn leaves, application of spores to leaves, and induction of the disease in the dark at high humidity and moderate temperatures. Infection and disease development were consistently achieved in four independent experiments on different corn hybrids and under different environmental conditions in a greenhouse and growth chamber. Disease induction was impacted by the source and storage conditions of spores, as tar spot was not induced with ascospores from leaves stored dry at 25 ºC for 5 months but was induced using ascospores from infected leaves stored at -20 ºC for 5 months. The time from inoculation to stromata formation was 10 to 12 days and ascospores were present 19 days after inoculation throughout our experiments. In addition to providing techniques that enable in-vitro experimentation, our research also provides fundamental insights into the conditions that favor tar spot epidemics.ConclusionsWe developed a method to reliably inoculate corn with P. maydis. The method was validated by multiple independent experiments in which infection was induced in 100% of the plants, demonstrating its consistency in controlled conditions. This new method facilitates research on tar spot and provides opportunities to study the biology of P. maydis, the epidemiology of tar spot, and for identifying host resistance.

A novel nepovirus causing a chlorotic fleck disease on common bean (Phaseolus vulgaris L.).

Two common bean leaf samples from Ethiopia that had shown chlorotic fleck and veinal mosaic symptoms but tested ELISA-negative for known viruses were mechanically transmitted to herbaceous hosts to obtain virus isolates ET-773/4 and ET-779. Virus purification from Chenopodium quinoa systemically infected with ET-773/4 yielded icosahedral particles measuring ~ 30 nm in diameter and containing a single capsid protein of ~ 58 kDa, suggesting a nepovirus infection. Analysis of nucleotide sequences generated from RNA1 and RNA2 of the isolates indicated that they represent a distinct virus species in the genus Nepovirus. Surprisingly, the most closely related sequence in the GenBank database was that of Hobart nepovirus 3, an incompletely described metagenomic sequence obtained from honey bees in Tasmania. This new nepovirus from Ethiopia is provisionally named "bean chlorotic fleck virus".

CHARACTERIZATION OF Exserohilum turcicum INFECTION SITES IN MAIZE GENOTYPES

ABSTRACT Northern leaf blight caused by Exserohilum turcicum is an important disease of maize (Zea mays L.), and its severity depends more closely on growth lesions than on spot number. Here, we characterized the infection sites of E. turcicum on resistant and susceptible maize genotypes by analyzing the histology of lesions as well as the structural and biochemical mechanisms of infection. Maize leaves were inoculated with the pathogen at specific points and incubated in a microhumidity chamber. Samples were obtained to follow fungal development and host tissue lignification using light and electron microscopy, and the activity and electrophoretic patterns of peroxidases were determined. The time course of spore germination and appressorium formation was essentially the same for both genotypes; however, a delay of 12 h in fungal penetration, accompanied by host tissue lignification, was noted in the resistant genotype, as opposed to that in the susceptible one. Scanning electron microscopy revealed fungal mycelium in the xylem vessels of both genotypes; however, in the resistant genotype, pathogen colonization was restricted to mesophyll cells around the penetration point, where chlorotic flecks were produced. Meanwhile, in the susceptible genotype, following penetration and chlorotic fleck formation, the pathogen continued to grow inside the xylem vessels and profusely colonized mesophyll tissue distant from the penetration point, resulting necrotic lesion development. Electrophoretic patterns of peroxidases were similar between the two genotypes, with three isoenzymes present in all tissues. In addition, two novel isoenzymes were detected in chlorotic flecks, necrotic lesions, and green tissue around the lesions.

Histopathological aspects of resistance in wheat to Puccinia triticina, induced by Pseudomonas protegens CHA0 and β-aminobutyric acid

After perception of specific biotic or abiotic stimuli, such as root colonization by rhizobacteria or selected chemicals, plants can enhance their basal resistance against pathogens. Due to its likely sustainability, this induced resistance will be valuable for disease management in agriculture. This study examined resistance against wheat leaf rust (Puccinia triticina) induced by Pseudomonas protegens CHA0 (CHA0) and β-aminobutyric acid (BABA). Seed dressing with CHA0 reduced the number of sporulating pustules on leaves, and expression of resistance was visible as necrotic or chlorotic leaf flecks. Beneficial effect of CHA0 on wheat seedlings growth was observed in when they were challenged or not with leaf rust. BABA was tested at 10, 15 or 20 mM, and a dose-dependent reduction of leaf rust infections was observed with greatest protection at 20 mM. However, BABA treatment repressed plant growth at 20 mM. Balancing the BABA impact on plant growth and its protective capacity, 15 mM of the compound was selected as suitable to protect wheat seedlings against leaf rust, with the least impact on vegetative host growth. Histological aspects of the pathogen infection process was studied to understand mechanisms of behind the observed resistance. The pre-entry process was not affected by the two resistance inducers, but both treatments reduced fungus penetration and haustorium formation. Timing and amplitude of the resistance reactions were different after bacterial or chemical induction, leading to different levels of resistance. During fungal colonization of host tissues, high deposition of callose and accumulation of H2O2 in both CHA0- and BABA-treated plants indicated important contributions to resistance.

Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays.

Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.

Viral diagnosis in cultivars of Ipomoea batatas (L.) Lam.

Ipomoea batatas (L.) Lam. commonly known as sweet potato, is an important staple food worldwide, mainly due to its high nutritional value and yield. However, vegetative reproduction of sweet potato makes it more susceptible to viral infections, which threatens its productivity, quality, and difficult long-term preservation in germplasm banks. Also, it can act as a virus reservoir infecting the rest of the plant accessions in the bank collections. Hence, this work aimed to screen Begomovirus, Potyvirus, and Carlavirus infections in 16 traditional sweet potato cultivars from the germplasm collection of the ISOPlexis Germplasm Bank, Madeira, Portugal. The infection prevalence by these viruses among cultivars was 81.25%, 25.00%, and 6.25%, respectively; being ISOP1011 the only accession coinfected by Potyvirus and Carlavirus. The accessions ISOP1006, ISOP1010, and ISOP1047 were also coinfected by Begomovirus and Potyvirus, highlighting their vulnerability to viral infections. The ISOP1005 and ISOP1027 accessions were the only ones not infected by any of these viruses. The analysis of the partial sequence obtained from the Carlavirus detected in the accession ISOP1011, revealed the existence of an ORF that encodes for 93 amino acids of the catalytic domain of an RNA-directed RNA polymerase related to the Tymovirus protein family, as could be confirmed by comparison with proteins stored in UniProtKB. Multiple sequence alignment with these proteins showed that Motifs A and B of the catalytic domain were conserved. The search for sequence similarity with sequences deposited in GenBank reported a high sequence identity with Sweet potato yellow mottle virus (SPYMV) and Sweet potato chlorotic fleck virus (SPCFV). However, the 9-11% discrepancy in nucleotide sequence identity and a phylogenetic analysis carried out using the maximum probability method suggests the virus isolated from ISOP1011 is a new divergent strain of the SPCFV species.

Orchid fleck virus and a novel strain of sweet potato chlorotic stunt virus associated with an ornamental cultivar of Alcea rosea L. in South Africa

Common hollyhock (Alcea rosea) is a ubiquitous ornamental in temperate climates but is highly adaptable and can be found growing in the tropics and subtropics. In 2019, an A. rosea plant showing symptoms of irregular chlorotic flecking on the basal leaves, with symptoms becoming gradually less severe toward the apex, was sampled in Pretoria, Gauteng province, South Africa. Total RNA was used to prepare an RNAtag-seq library, which was sequenced using an Illumina HiSeq 2500 instrument. Subsequent analysis of the data revealed the presence of two bipartite RNA viruses, namely orchid fleck virus (OFV) (segment 1: MW073772; segment 2: MW073773) and sweet potato chlorotic stunt virus (SPCSV) (segment 1: MW073774; segment 2: MW073775). OFV from this study was closely related to a strain from South Africa, associated with citrus leprosis disease, while SPCSV represented a novel strain. RT-PCR and bidirectional Sanger sequencing were used to confirm the presence of both viruses. Further samples were collected in 2020, which showed severe interveinal chlorosis, and were tested with RT-PCR; however only SPCSV was associated with these plants. This is the first time that both viruses have been associated with A. rosea, which should be considered a potential reservoir host of these agriculturally important viruses.

Quantitative detection of Exserohilum turcicum in northern leaf blight diseased sorghum and maize leaves

Exserohilum turcicum is the causal agent of northern leaf blight (NLB) disease in sorghum and maize. Early detection of this economically important pathogen is essential for effective disease management to limit yield losses. Here we present a real-time quantitative PCR (qPCR) assay specific for E. turcicum detection and biomass quantification in sorghum and maize. In planta fungal quantification was achieved through amplification of a cytochrome P450 oxidoreductase (cpr1) gene fragment and subsequent normalisation to the host glutathione S-transferase III gene (gst3). The assay could specifically detect E. turcicum in sorghum and maize, but the cpr1 gene fragment was not amplified in non-target fungal pathogens. Application of the assay with NLB diseased sorghum and maize leaf material revealed a significant increase in E. turcicum DNA in leaves with lesion symptoms when compared to leaves with early stage chlorotic fleck symptoms in both hosts. Furthermore, E. turcicum was detected at levels as low as 1 pg in infected sorghum and maize leaves. The assay enables rapid detection and quantification of E. turcicum in sorghum and maize and has useful applications in crop breeding programmes and disease management where cultivar selection and early detection of the pathogen are essential to limit disease spread.

Association of two novel viruses with chlorotic fleck disease of ginger

AbstractChlorotic fleck disease of ginger, the causal virus of which was unknown so far is an important production constraint of ginger in India and other parts of the world. In the present study, two new RNA viruses were discovered in chlorotic fleck affected plant by the virome analysis using high‐throughput sequencing (HTS) of small RNA and transcriptome. The HTS results were verified through reverse transcriptase polymerase chain reaction (RT‐PCR) using total RNA from infected plants and primers designed from the contigs. Cloning and sequencing of the RT‐PCR products of one of the viruses resulted in a sequence of 4,143 bases that showed similarities to panicoviruses and machlomoviruses. The complete genome of this virus contained six open reading frames (ORFs) that potentially encode proteins of 43, 104, 8, 7, 15 and 27 kDa. Based on the genomic and phylogenetic analysis, this virus is predicted to be a new member of the family Tombusviridae for which the name ginger chlorotic fleck‐associated virus 1 is proposed. Similarly, cloning and sequencing of the RT‐PCR products of the other virus resulted in a sequence of 5,514 bases that showed similarities to ampeloviruses. Based on the genomic and phylogenetic analysis, this virus is predicted to be a new member of the genus Ampelovirus for which the name ginger chlorotic fleck‐associated virus 2 is proposed. Reliable RT‐PCR and SYBR Green‐based quantitative RT‐PCR assays were developed for the detection of both viruses in plants that would aid in the identification and propagation of virus‐free ginger plants. Additional investigations are required to elucidate the relationship between the symptoms and viral infections.

Identification of Berberis spp. as Alternate Hosts for Puccinia achnatheri-sibirici Under Controlled Conditions and Morphologic Observations of Sexual Stage Development of the Rust Fungus.

Gramineous grasses are a large group of species, many of which act as accessory (secondary) host for a large number of rust fungi, including devastating rust pathogens of cereals. Among the rust fungi, some are known to be heteroecious and have a complete macrocyclic life cycle with five types of spores on distinct plant species, but for many others the complete life cycle is unknown. Puccinia achnatheri-sibirici, a rust fungus infecting grasses in the genus Achnatherum, has been known for only its uredinial and telial stages; however, the other (pycnial and aecial) stages have not been identified. In this study, we demonstrate that P. achnatheri-sibirici is a heteroecious, macrocyclic fungus with the sexual stage on barberry (Berberis spp.) through inoculation. Pycnia and aecia were successively produced on the inoculated barberry plants. Inoculation of Achnatherum extremiorientale leaves with aeciospores produced yellow-orange uredinia with high infection types, whereas inoculation of wheat variety Mingxian 169, highly susceptible to Puccinia striiformis f. sp. tritici which causes stripe rust on wheat, produced chlorotic flecks but no uredinia. The ITS sequence analysis of P. achnatheri-sibirici did not match with any sequence in the NCBI database and had the highest homology with 94% compared to Puccinia brachypodii and Puccinia aizazii. Observations of the uredinial, telial, and basidial stages on A. extremiorientale and pycnial and aecial stages on Berberis shensiana using light and scanning electron microscopes revealed its characteristics. Morphological characteristics of urediniospores and teliospores are most similar with those of P. achnatheri-sibirici described in the literature. This study proved (1) the life cycle of P. achnatheri-sibirici as heteroecious and macrocyclic and the alternate host as barberry; (2) the description of life stages in the sexual cycle, especially the morphologies of aecial, pycnial, and basidial stages; and (3) the expansion of knowledge on the rust flora on barberry.

Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays for the detection of two novel viruses infecting ginger

Our recent studies have shown the association of two novel viruses namely, ginger chlorotic fleck-associated virus 1 (GCFaV-1) and ginger chlorotic fleck-associated virus 2 (GCFaV-2) with chlorotic fleck disease of ginger. As ginger is propagated through vegetative means, the development of diagnostics would aid in the identification of virus-free plants. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays were developed and validated for the quick detection of GCFaV-1 and GCFaV-2. The detection limits of viruses by these assays, when compared with conventional and real-time RT-PCR, showed that RT-LAMP was up to 1000 times more sensitive than conventional RT-PCR and one-hundredth that of real-time RT-PCR for both the viruses. The detection limit of RT-RPA for GCFaV-1 was up to 100 times more than that of RT-PCR and one-thousandth that of real-time RT-PCR. On the other hand, for detecting GCFaV-2, RT-RPA was found up to 1000 times more sensitive than conventional RT-PCR and one hundredth that of real-time RT-PCR. Based on the cost-effectiveness and duration, RT-LAMP and RT-RPA assays can be suggested for the rapid detection of both viruses.

Emergence of Puccinia graminis Causing Orchardgrass (Dactylis glomerata) Rust in China

Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season perennial forage grasses around the world and has been widely cultivated in China. Since 2007, a rust was observed on orchardgrass in Chongqing municipality and Sichuan province, China. In May 2018, 85% incidence of the rust was observed in an orchardgrass genetic resources field (29.40 ° N; 105.58 ° E; 296.1 m elevation) in Rongchang district, Chongqing. The disease on orchardgrass is characterized by small, light yellow to yellowish-brown, nearly circular uredia (0.75 to 1.03 × 1.21 to 3.84 mm) surrounded by chlorotic spots, appearing on both sides of leaf, leaf sheath, stem, and inflorescence. Urediniospores were subglobose or ellipsoid monospores, yellow or yellow-brown, 17 to 19 × 22 to 28 μm, with echinulate spines on the surface and three or four germ tube pores distributed equatorially. Telia were rarely observed. Teliospores were smooth, yellowish-brown, club-shaped, twin cells, constricted at the septa, with an obvious stalk, 26 to 41 × 16 to 20 μm. Teliospore wall thicknesses were 1 to 2 μm at the side and 5 to 8 μm at the apex. To support the morphological identification, molecular phylogenetic procedures were applied. Genomic DNA was extracted from urediniospores on infected leaves of orchardgrass. PCR was used to amplify the ITS rDNA region, the 5′ end of the nuclear ribosomal large subunit (28S) and partial beta-tub1 gene sequence (Aime et al. 2018; van der Merwe et al. 2007). A comparison with the GenBank sequences revealed that the ITS, 28S, and beta-tub1 gene sequences were 99.84, 99.70, and 99.38% identical, respectively, to those of Puccinia graminis (GenBank DQ417384.1, HQ412648.1, and HQ317589.1). Homology was also confirmed by analysis of a phylogenetic tree constructed by MEGA7. Representative sequences were deposited in GenBank (accession nos. MH638997.1, MK952783, and MK952781). On the basis of morphology and sequence comparisons, the pathogen was identified as P. graminis (Wang and Zhuang 1998). Rust specimens have been kept in the Forage Specimen Room of Southwest University. Pathogenicity was demonstrated by brushing fresh urediniospores from rusted leaves directly onto the leaves of healthy orchardgrass grown in pots. Control plants were inoculated with sterile water. All pots were kept in a plant growth chamber (20°C, 100% relative humidity) for 24 h and left under glasshouse conditions. Initial symptoms of single chlorotic flecks appeared 4 to 5 days after inoculation. On the seventh day, the host epidermis began to bulge, and within 2 weeks, the epidermis ruptured and showed yellow to brown uredia. Control plants remained symptomless. The rust fungus P. graminis is an important pathogen of orchardgrass, which has been found in 30 countries in the world (Farr and Rossman 2019). However, this is the first report of this fungus causing rust disease on orchardgrass in China. It is anticipated that plants would eventually die under heavy infection, so this fungus potentially could pose a significant threat to local orchardgrass production.

Prevalence, epidemiology and molecular studies of Tomato chlorosis virus (ToCV) in South Africa.

Criniviruses accumulate in the phloem tissue and damage crops by reducing chlorophyll which is essential for plant growth and development. Tomato chlorosis crinivirus (ToCV) is vectored by several whitefly species that damage tomato crops throughout the world. In South Africa, ToCV is a poorly studied pathogen of global economic importance. Therefore, a national survey was initiated to investigate the occurrence and distribution of criniviruses infecting tomato crops in South Africa. Whitefly infested tomato crops exhibiting interveinal leaf chlorosis and chlorotic flecking symptoms were assayed for crinivirus infections using a multiplex reverse transcription polymerase reaction (RT-PCR) approach to assess for the presence of crinivirus species that are known to infect solanaceous hosts. Next-generation sequencing (NGS) was used to generate the complete genome of ToCV from South Africa. Results from the survey indicated that ToCV is presently the only crinivirus species infecting tomatoes in South Africa. Blast analysis showed that the RNA-1 segment of ToCV from South Africa (ToCR1-186) matched 99% to Spanish isolates. On the other hand, the RNA-2 (ToCR2-186) segment matched 98% to a South Korean isolate and three Spanish isolates. Although recombination events were not detected, phylogenetic studies showed inconsistencies in the grouping of RNA-1 and RNA-2 segments for some of the ToCV isolates analyzed in this study. Therefore, we suggest the possibility of intraspecific reassortment. This is the first comprehensive study and full genome sequence of ToCV from South Africa. The information generated from this study is intended to raise awareness of ToCV infections on tomato crops in South Africa.

Prevalence of sweetpotato viruses in Acholi sub-region, northern Uganda

The purpose of the study was to identify different viruses infecting sweetpotato and the level of co-infection and spatial distribution of the viruses within the Acholi sub-region of northern Uganda. Multiplex PCR was used to screen and determine level of co-infection in 380 sweetpotato plants. The PCR scores were computed to give overall frequency of occurrence of different viruses. The spatial distribution of viruses was represented on an ArcGIS map. Of all screened samples, 24% (92/380) were infected with at least one virus. Sweetpotato feathery mottle virus (65/92), sweetpotato chlorotic fleck virus (17/92) and sweetpotato mild mottle virus (8/92) were the most frequent viruses detected. Of sampled fields, 74% (28/38) had at least one virus-infected sweetpotato plant. The four viruses detected are the major viruses causing significant yield losses in major sweetpotato growing regions of Uganda and East Africa. The findings of limited distribution and low prevalence of the viruses in the region indicate it causes less burden to sweetpotato production in the sub-region compared with other parts of Uganda.

A histological assessment of the infection strategy of Exserohilum turcicum in maize

Northern leaf blight is a lethal foliar disease of maize caused by the fungus Exserohilum turcicum. The aim of this study was to elucidate the infection strategy of the fungus in maize leaves using modern microscopy techniques and to understand better the hemibiotrophic lifestyle of E. turcicum. Leaf samples were collected from inoculated B73 maize plants at 1, 4, 9, 11, 14 and 18 days post‐inoculation (dpi). Samples were prepared according to standard microscopy procedures and analysed using light microscopy as well as scanning (SEM) and transmission electron microscopy (TEM). Microscopic observations were preceded by macroscopic observations for each time point. The fungus penetrated the leaf epidermal cells at 1 dpi and the disease was characterized by chlorotic leaf flecks. At 4 dpi the chlorotic flecks enlarged to form spots, and at 9 dpi hyphae were seen in the epidermal cells surrounding the infection site. At 11 dpi lesions started to form on the leaves and SEM revealed the presence of hyphae in the vascular bundles. At 14 dpi the xylem was almost completely blocked by hyphal growth. Hyphae spread into the adjacent bundle sheath cells causing cellular damage, characterized by plasmolysis, at 18 dpi and conidiophores formed through the stomata. Morphologically, lesions started to enlarge and coalesce leading to wilting of leaves. This study provides an updated, detailed view of the infection strategy of E. turcicum in maize and supports previous findings that E. turcicum follows a hemibiotrophic lifestyle.

Complete Genome Sequence Analysis of Two Divergent Groups of Sweet potato chlorotic fleck virus Isolates Collected from Korea.

The Sweet potato chlorotic fleck virus (SPCFV), of the genus Carlavirus (family Betaflexiviridae), was first detected as one of several viruses infecting sweet potatoes (Ipomea batatas L.) in Korea. Out of 154 sweet potato samples collected in 2012 that were showing virus-like symptoms, 47 (31%) were infected with SPCFV, along with other viruses. The complete genome sequences of four SPCFV isolates were determined and analyzed using previously reported genome sequences. The complete genomes were found to contain 9,104-9,108 nucleotides, excluding the poly-A tail, containing six putative open reading frames (ORFs). Further, the SPCFV Korean isolates were divided into two groups (Group I and Group II) by phylogenetic analysis based on the complete nucleotide sequences; Group I and Group II had low nucleotide sequence identities of about 73%. For the first time, we determined the complete genome sequence for the Group II SPCFV isolates. The amino acid sequence identity in coat proteins (CP) between the two groups was over 90%, whereas the amino acid sequence identity in other proteins was less than 80%. In addition, SPCFV Korean isolates had a low amino acid sequence identity (61% CPs and 47% in the nucleotide- binding protein [NaBp] region) to that of Melon yellowing-associated virus (MYaV), a typical Carlavirus.

Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya.

Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I–III) while four well-supported clades were resolved in SPVC (I–IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.

Diseases infecting ginger (Zingiber officinale Roscoe): A review

Ginger (Zingiber officinale Roscoe) is an important spice crop in India, which is also one of the leading producer and exporter of ginger in the world. During cultivation, the crop is severely infected by various diseases of them soft rot, yellows, Phyllosticta leaf spot, storage rot, bacterial wilt, mosaic, chlorotic fleck are important. These diseases reduce the potential yields drastically. The geographical distribution, losses, symptoms, causal organism, disease cycle, epidemiology and host resistance, cultural, biological, chemical and integrated management of above mentioned diseses have been discussed in the present paper.

Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa.

Viruses infecting wild flora may have a significant negative impact on nearby crops, and vice-versa. Only limited information is available on wild species able to host economically important viruses that infect sweetpotatoes (Ipomoea batatas). In this study, Sweet potato chlorotic fleck virus (SPCFV; Carlavirus, Betaflexiviridae) and Sweet potato chlorotic stunt virus (SPCSV; Crinivirus, Closteroviridae) were surveyed in wild plants of family Convolvulaceae (genera Astripomoea, Ipomoea, Hewittia and Lepistemon) in Uganda. Plants belonging to 26 wild species, including annuals, biannuals and perennials from four agro-ecological zones, were observed for virus-like symptoms in 2004 and 2007 and sampled for virus testing. SPCFV was detected in 84 (2.9%) of 2864 plants tested from 17 species. SPCSV was detected in 66 (5.4%) of the 1224 plants from 12 species sampled in 2007. Some SPCSV-infected plants were also infected with Sweet potato feathery mottle virus (SPFMV; Potyvirus, Potyviridae; 1.3%), Sweet potato mild mottle virus (SPMMV; Ipomovirus, Potyviridae; 0.5%) or both (0.4%), but none of these three viruses were detected in SPCFV-infected plants. Co-infection of SPFMV with SPMMV was detected in 1.2% of plants sampled. Virus-like symptoms were observed in 367 wild plants (12.8%), of which 42 plants (11.4%) were negative for the viruses tested. Almost all (92.4%) the 419 sweetpotato plants sampled from fields close to the tested wild plants displayed virus-like symptoms, and 87.1% were infected with one or more of the four viruses. Phylogenetic and evolutionary analyses of the 3′-proximal genomic region of SPCFV, including the silencing suppressor (NaBP)- and coat protein (CP)-coding regions implicated strong purifying selection on the CP and NaBP, and that the SPCFV strains from East Africa are distinguishable from those from other continents. However, the strains from wild species and sweetpotato were indistinguishable, suggesting reciprocal movement of SPCFV between wild and cultivated Convolvulaceae plants in the field.

Complete Genome Sequences of the Carlavirus Sweet potato chlorotic fleck virus from East Timor and Australia.

We present here the first complete genome sequences of Sweet potato chlorotic fleck virus (SPCFV) from sweet potato in Australia and East Timor, and we compare these with four complete SPCFV genomes from South Korea and one from Uganda. The Australian, East Timorese, South Korean, and Ugandan genomes differed considerably from each other.