Host range, purification, and genetic variability in Sweet potato chlorotic fleck virus

Sweet potato chlorotic fleck virus (SPCFV) has recently been classified as a putative new member of the genus Carlavirus (family Flexiviridae) on the basis of its molecular properties. In this study, SPCFV was characterized in terms of host range, physical and biological characteristics, and genetic variability. In addition to sweet potato, SPCFV infected some plant species in the families Convolvulaceae, Chenopodiaceae, and Solanaceae. Limited numbers of virus particles were observed in the assimilation parenchyma cells of infected plant tissues; some cells had a distorted and enlarged endoplasmic reticulum though without any cytoplasmic and amorphous inclusions. The normal length of SPCFV particles was determined to be approximately 800 nm. In enzyme-linked immunosorbent assays, polyclonal antibodies raised against purified SPCFV virions were able to detect the virus in infected sweet potato and indicator plant tissues. In immunoelectron microscopy, SPCFV particles were all strongly decorated when reacted with homologous antiserum. Comparison of the 3′ terminal part of the genome of a range of geographically diverse isolates revealed a high level of genetic diversity. The amino acid sequence identity in the coat protein and the nucleic acid binding protein ranged from 89 to 99.7% and from 75.9 to 99.2%, respectively. Phylogenetic analysis of both proteins showed a geographically associated clustering into two genogroups

Genetic homogeneity among Ugandan isolates of Xanthomonas campestris pv. musacearum revealed by randomly amplified polymorphic DNA analysis

The Random Amplification of Polymorphic DNA (RAPD) analysis was used to detect the genetic diversity among Ugandan isolates of Xanthomonas campestris pv. musacearum (Xcm), the causal agent of banana Xanthomonas wilt (BXW) disease. Seven random primers were used because of their ability to amplify reproducible and reliable fingerprints generated between 6 - 12 amplicons each from the Xcm isolates obtained from central core of pseudostems, peduncles, fruit peelings, sap, nectar,insects’ bodies and bacterial oozes. Regardless of the source and geographical origin, similar fingerprints were generated from the tested isolates. Using a similarity coefficient of 58%, the unweighted pair group method with arithmetic averaging (UPGMA) analysis did not reveal anysignificant differences in clustering, with exception of a single isolate that had unique fingerprints. Prior to the genetic analysis, all the isolates compared showed no significant difference (P = 0.92) with regardto incubation period for appearance of symptoms and the severity of symptoms in pathogenicity test. Thus, our data indicates that the population of Xcm in Uganda is clonal, that is, one uniform populationbeing spread fast and efficiently, suggesting that there is a low likelihood of the current population to rapidly evolve, in the near future, into more virulent strains to overcome any resistance deployed

Rep-PCR reveals a high genetic homogeneity among Ugandan isolates of Xanthomonas campestris pv musacearum

Wilting of plants incited by a bacterium, Xanthomonas campestris pv musacearum (Xcm), was first described on Ensete (Ensete ventricosum) and later bananas (Musa species) in the highlands ofEthiopia in 1968. Although the spread outside Ethiopia remained unreported for several decades, an epidemic of the disease on banana in Uganda was observed in 2001, in the districts of Mukono andKayunga. Since then, the disease has spread into almost three quarters of the major banana growing areas in Uganda. It has also been confirmed affecting banana plantations in the Democratic Republic ofCongo (DRC) and Rwanda. Repetitive sequence based genomic fingerprinting that uses a PCRmediated amplification of DNA sequences located between specific interspersed sequences of highlyconserved elements in prokaryotic genomes was used to characterize a collection of Xcm isolates from banana in Uganda. Fingerprints of bacterial isolates collected from Xcm symptom bearing bananaplants grown in production fields from 10 districts including Kayunga, Masindi, Luwero, Kampala, Kiboga, Lira, Wakiso, Kibale and Nakasongola revealed similar patterns. Cluster analysis of pair wisesimilarity values performed using unweighted pair group method with arithmetic averages clustering technique did not generate any differences in the fingerprint patterns either. The implications of thisgenetic homogeneity on the origin and management of Xcm is discussed here

Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050-1065

Published ErratumThis is the final version of the article. Available from MDPI via the DOI in this record.NOTE: the original article is in ORE at http://hdl.handle.net/10036/3880Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. [...]

The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda.

types: Journal ArticleThis is a pre-copyedited, author-produced PDF of an article accepted for publication in FEMS following peer review. The version of record Aritua, V., Musoni, A., Kabeja, A., Butare, L., Mukamuhirwa, F., Gahakwa, D., . . . Smith, J. (2015). The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda, FEMS Microbiology Letters, 2015, Vol. 362, No. 4 pp. 1-4 is available online at: http://femsle.oxfordjournals.org/content/362/4/1.1.exploreWe announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.Canadian International Development AgencyBBSRC SCPRI

Do Native Parasitic Plants Cause More Damage to Exotic Invasive Hosts Than Native Non-Invasive Hosts? An Implication for Biocontrol

Field studies have shown that native, parasitic plants grow vigorously on invasive plants and can cause more damage to invasive plants than native plants. However, no empirical test has been conducted and the mechanism is still unknown. We conducted a completely randomized greenhouse experiment using 3 congeneric pairs of exotic, invasive and native, non-invasive herbaceous plant species to quantify the damage caused by parasitic plants to hosts and its correlation with the hosts' growth rate and resource use efficiency. The biomass of the parasitic plants on exotic, invasive hosts was significantly higher than on congeneric native, non-invasive hosts. Parasites caused more damage to exotic, invasive hosts than to congeneric, native, non-invasive hosts. The damage caused by parasites to hosts was significantly positively correlated with the biomass of parasitic plants. The damage of parasites to hosts was significantly positively correlated with the relative growth rate and the resource use efficiency of its host plants. It may be the mechanism by which parasitic plants grow more vigorously on invasive hosts and cause more damage to exotic, invasive hosts than to native, non-invasive hosts. These results suggest a potential biological control effect of native, parasitic plants on invasive species by reducing the dominance of invasive species in the invaded community

Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer

Molecular diversity in sweet potato infecting viruses in Africa: With emphasis on Sweet potato chlorotic fleck virus

No Abstract

THE PERSPECTIVE OF SWEETPOTATO CHLOROTIC STUNT VIRUS IN SWEETPOTATO PRODUCTION IN AFRICA: A REVIEW

Sweetpotato chlorotic stunt virus (SPCSV) (Crinivirus: Closteroviridae) occurs in the main tropical regions of the World and is probably the most damaging pathogen of sweetpotato (Ipomea batatas   ). However, until recently, little research had been done on it. The methods of identification were inadequate and this led to synonymy. The virus is transmitted by the whitefly species, Bemisia tabaci   and Trialeurodes abutilonea   , in a semi-persistent fashion. At least two serotypes occur, one, first described from West Africa (SPCSVWA ), and the other first described from East Africa (SPCSVEA ). Both serotypes have also been found in the Americas. Nucleotide sequencing has facilitated the process of distinguishing strains. The SPCSV may have originated along with sweetpotato in the Americas, but is perhaps more likely to have been a 'new encounter' for sweetpotato when it was introduced to Africa and elsewhere in the 'Old World'. It infects few plant species other than Ipomoea   spp. The virions comprise long flexuous particles and the genome is RNA and bipartite. Geographically, isolated strains of SPCSV have been distinguished using serological- and nucleic acid-based methods. The virus synergises Sweetpotato feathery mottle virus (SPFMV) (Potyvirus: Potyviridae), leading to increased titres of this virus and the development of the severe disease sweetpotato virus disease (SPVD) in dually infected sweetpotato plants. Plants affected by SPVD following artificial or natural infection with SPCSV plus SPFMV have generally yielded c.60 -90% less than uninfected or unaffected controls in field trials; plants infected with SPCSV alone generally yielded c.30 - 80% less. However, in crops, compensatory growth by unaffected neighbouring sweetpotato plants probably results in direct effects on overall crop yields being small, and the major effect of SPCSV in constraining the yields of sweetpotato is perhaps through preventing the cultivation of high yielding but SPVD-susceptible sweetpotato cultivars. Breeding resistant high-yielding varieties has been the main means of avoiding the deleterious effects of SPVD. Although sweetpotato cultivars which have field resistance to SPCSV have been identified, no gene conferring immunity to SPCSV has been identified within sweetpotato or its close relatives. Cultivars non-indigenous to Africa seem particularly susceptible. Extreme resistance has been identified in certain wild Ipomoea   spp. Recent epidemiological studies indicate that most spread of SPCSV is short distance, leading to interest in the use of phytosanitation measures to grow high-yielding but somewhat SPVD-susceptible cultivars. This paper comprises a review of research work done on SPCSV world wide dating from 1939 to-date

Use of Herbicides for Control of Banana Bacterial Wilt in Uganda

The potential of herbicides for destroying banana plants infected with bacterial wilt has been evaluated. Experiments were conducted on station at Kawanda Agricultural Research Institute (KARI) and on-farm at Nekoyedde and Kimenyedde, in Mukono district. Two systemic herbicides, Glyphosate and 2, 4-D were evaluated for their effectiveness in destroying infected banana plants. Selected plants were injected with 20ml of herbicide in water at the rate of 1:20 administered in a perforated hole at the collar base of the pseudostem close to the corm using a sharp pencil-size metallic rod. All plants injected with 2,4-D herbicide snapped and died within 30-60 days while plants injected with glyphosate wilted and dried up within 90-120 days. Both herbicides were able to kill at least 85% of the plants. Plant destruction depended on herbicide dose, mat size and nature of suckering. Re-suckering rates between the two herbicides did not significantly differ. The mean re-suckering on farmer's fields was 1.5% for glyphosate and 7.2% for 2,4-D compared to 15.2% and 11.3% on the station. Herbicides were able to destroy plants within radius of 16.8 ± 1.76 cm from the injected plant per mat. Higher doses killed faster and better but it was not clear why very high doses caused high re-suckering. It was therefore concluded that although 2,4-D herbicide destroyed banana mats faster than Glyphosate, in the long run however, the efficiencies of kill between the two herbicides do not differ significantly. Both herbicides showed great potential for use as an option for removal or destruction of diseased plants. However, considering environmental safety issues, Glyphosate is recommended for farmer use in Uganda