'Bunchy top symptom' of papaya in Cuba: new insights

Papaya is an important export crop in Cuba. A disease named Bunchy top symptom (BTS) was first observed in 2003 from Villa Clara province, but is now widespread throughout the country. A nested PCR assay with 16S rDNA phytoplasma primers P1/P7 and R16F2n/R2 was used to index more than 2200 papaya plants, weeds and insect samples collected between November 2005 and June 2006. RFLP patterns for all amplicons were identical with HaeIII, RsaI and AluI enzymes. No rickettsia-like bacteria were found in any of the samples. Phytoplasma rDNA was amplified from 1449 (89.7%) papaya plants with BTS symptoms. Phytoplasma rDNA was also detected in 331 apparently healthy papayas, and other plant species: Anoda acerifolia (57), Euphorbia heterophylla (73), Malvastrum coromandelianum (41) and Rynchosia minima (37) and 60/75 batches of Empoasca papayae. Sequences from the phytoplasma in papaya (DQ868531), A. acerifolia (DQ286950); E. heterophylla (DQ286951); M. coromandelianum (DQ286952); R. minima (DQ868533) and the leafhopper E. papayae (DQ868532) all showed 99% similarity to the phytoplasma associated with polygala phyllody, PPhy, (AY787140) belonging to the 16SrII group, ‘Candidatus Phytoplasma aurantifolia’. The discovery of the BTS phytoplasma in weed species and a putative vector Empoasca papayae suggests, that these plants and the leafhopper may have role in the spread of this disease

From coconut to cassava: the coconut lethal yellowing phytoplasma is worsening the threat to food security in C\uf4te d\u2019Ivoire

Background. Cassava (Manihot esculenta Crantz) is a major staple food in the developing countries whose total world production reached approximately 278 million metric tonnes in 2017. C\uf4te d'Ivoire produces around three million tonnes of cassava every year and reached 4.54 metric tonnes in 2017. It is typically consumed as 'attiek\ue9', which is currently exported on regional and international markets. Cassava crop is now threaten by the C\uf4te d'Ivoire lethal yellowing disease (CILY) first reported and associated with a phytoplasma in Grand-Lahou in 2013. CILY destroyed over 400 ha of coconut groves in smallholder coconut farms where women farmers started planting cassava as an alternative food and cash crop in coconut lands devastated by the disease. Methods. Symptoms of leaf mosaic, curling and yellowing were observed in cassava orchards intwo coconut-growing villages located in the south coastal littoral of Grand-Lahou. Leaf samples were collected from symptom-bearing and symptomless cassava plants and subjected to total DNA extraction. PCR with phytoplasma universal 16S rRNA primers, and group-specific primers for subgroup 16SrXXII-B, \u2018Candidatus Phytoplasma palmicola\u2019-related strains; and with specific primers for African/Eastern cassava mosaic viruses (ACMV, EACMV). Amplicons were purified, cloned and sequenced. Sequences were compared to those of reference in NCBI (https://www.ncbi.nlm.nih.gov) and used for phylogeny analysis of phytoplasma and virus strains, respectively. Results. Phytoplasma DNA was amplified from six out of 12 symptom-bearing samples, five of which co-amplified virus DNA. Phytoplasma sequences showed 99% identity to those of 16SrXXII-B phytoplasmas as confirmed through phylogeny analysis. One cassava plant was co-infected with ACMV, closely related to the Angola strain, while the other four showed co-infection with both the ACMV (Angola) and an EACMV strain from Madagascar. All cassava varieties were phytoplasma-begomovirus co-infected, except the Yac\ue9 variety. Conclusions. Cassava plants in Grand-Lahou orchards were found infected by CILY phytoplasma (group 16SrXXII-B) and ACMV/EACMV virus strains. Results indicate that cassava may be an alternative host for the CILY phytoplasma, which may play a role spreading and worsening CILY epidemic. Prompt actions are required while waiting for a suitable resistant coconut cultivar. Short-term solutions may include replanting cassava yards with newly developed cassava varieties that enhance plant resilience against the coconut phytoplasma and ACMV/EACMV viruses to help supporting food production and improve livelihoods of smallholder coconut farmers in Grand-Lahou

Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium

AbstractOver 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastix sensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerina indica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae

First report of a phytoplasma affecting cassava orchards in Cote d'Ivoire

Annex 46 of 48 for CIFSRF-IDRC/GAC Final technical report: http://hdl.handle.net/10625/56415This work was carried out with the aid of a grant from Canada’s International Development Research Centre (IDRC), and with financial support from the Government of Canada, provided through Global Affairs Canada (GAC)This is the first report of a phytoplasma affecting cassava in Côte d'Ivoire. The findings suggest that cassava may be a potential alternative host for the Côte d'Ivoire lethal yellowing (CILY) phytoplasma, which poses a serious threat for the food security of smallholder coconut and cassava farmers, especially women, in Grand-Lahou, Côte d’Ivoire. Leaf samples were collected at random from 12 symptom-bearing and two symptomless cassava plants from two villages. Illustrations/ figures depict the symptoms of yellowing. Cassava (Manihot esculenta) is one of the staple foods in Africa, cultivated in 40 countries and producing more than three million tonnes per year

The repulsive lattice gas, the independent-set polynomial, and the Lov\'asz local lemma

We elucidate the close connection between the repulsive lattice gas in equilibrium statistical mechanics and the Lovasz local lemma in probabilistic combinatorics. We show that the conclusion of the Lovasz local lemma holds for dependency graph G and probabilities {p_x} if and only if the independent-set polynomial for G is nonvanishing in the polydisc of radii {p_x}. Furthermore, we show that the usual proof of the Lovasz local lemma -- which provides a sufficient condition for this to occur -- corresponds to a simple inductive argument for the nonvanishing of the independent-set polynomial in a polydisc, which was discovered implicitly by Shearer and explicitly by Dobrushin. We also present some refinements and extensions of both arguments, including a generalization of the Lovasz local lemma that allows for "soft" dependencies. In addition, we prove some general properties of the partition function of a repulsive lattice gas, most of which are consequences of the alternating-sign property for the Mayer coefficients. We conclude with a brief discussion of the repulsive lattice gas on countably infinite graphs.Comment: LaTex2e, 97 pages. Version 2 makes slight changes to improve clarity. To be published in J. Stat. Phy

Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)

Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html

Dispersal of Adult Black Marlin (Istiompax indica) from a Great Barrier Reef Spawning Aggregation

The black marlin (Istiompax indica) is one of the largest bony fishes in the world with females capable of reaching a mass of over 700 kg. This highly migratory predator occurs in the tropical regions of the Pacific and Indian Oceans, and is the target of regional recreational and commercial fisheries. Through the sampling of ichthyoplankton and ovaries we provide evidence that the relatively high seasonal abundance of black marlin off the Great Barrier Reef is, in fact, a spawning aggregation. Furthermore, through the tracking of individual black marlin via satellite popup tags, we document the dispersal of adult black marlin away from the spawning aggregation, thereby identifying the catchment area for this spawning stock. Although tag shedding is an issue when studying billfish, we tentatively identify the catchment area for this stock of black marlin to extend throughout the Coral Sea, including the waters of Papua New Guinea, the Solomon Islands, Micronesia, New Caledonia, Kiribati, Vanuatu, Fiji, Tuvalu and Nauru

Distribution and Habitat Associations of Billfish and Swordfish Larvae across Mesoscale Features in the Gulf of Mexico

Ichthyoplankton surveys were conducted in surface waters of the northern Gulf of Mexico (NGoM) over a three-year period (2006–2008) to determine the relative value of this region as early life habitat of sailfish (Istiophorus platypterus), blue marlin (Makaira nigricans), white marlin (Kajikia albida), and swordfish (Xiphias gladius). Sailfish were the dominant billfish collected in summer surveys, and larvae were present at 37.5% of the stations sampled. Blue marlin and white marlin larvae were present at 25.0% and 4.6% of the stations sampled, respectively, while swordfish occurred at 17.2% of the stations. Areas of peak production were detected and maximum density estimates for sailfish (22.09 larvae 1000 m−2) were significantly higher than the three other species: blue marlin (9.62 larvae 1000 m−2), white marlin (5.44 larvae 1000 m−2), and swordfish (4.67 larvae 1000 m−2). The distribution and abundance of billfish and swordfish larvae varied spatially and temporally, and several environmental variables (sea surface temperature, salinity, sea surface height, distance to the Loop Current, current velocity, water depth, and Sargassum biomass) were deemed to be influential variables in generalized additive models (GAMs). Mesoscale features in the NGoM affected the distribution and abundance of billfish and swordfish larvae, with densities typically higher in frontal zones or areas proximal to the Loop Current. Habitat suitability of all four species was strongly linked to physicochemical attributes of the water masses they inhabited, and observed abundance was higher in slope waters with lower sea surface temperature and higher salinity. Our results highlight the value of the NGoM as early life habitat of billfishes and swordfish, and represent valuable baseline data for evaluating anthropogenic effects (i.e., Deepwater Horizon oil spill) on the Atlantic billfish and swordfish populations