Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.     

Evaluation of Whatman FTA cards for the preservation of yellow fever virus RNA for use in molecular diagnostics

Yellow fever virus (YFV) is a flavivirus that frequently causes outbreaks of hemorrhagic fever in Africa and South America and is considered a reemerging public health threat. Accurate diagnosis of yellow fever (YF) disease is critical as one confirmed case constitutes an outbreak and may trigger a mass vaccination campaign. Highly sensitive and specific molecular diagnostics have been developed; however, these assays require maintenance of cold-chain during transport of specimens to prevent the degradation of viral RNA prior to testing. Such cold-chain requirements are difficult to meet in some regions. In this study, we investigated Whatman FTA cards as an alternative stabilization method of YFV RNA for use in molecular diagnosis. Using contrived specimens, linear regression analysis showed that RNA detection from a single 6mm FTA card punch was significantly less sensitive than traditional RNA extraction; however, pooling RNA extracted from two FTA punches significantly lowered the limit of detection to be equal to that of the traditional RNA extraction gold standard. In experiments addressing the ability of FTA card methodology to stabilize YFV RNA at variable temperature, RNA could be detected for more than two weeks following storage at 25°C. Even more promising, YFV RNA was detectable on cards held at 37°C from two days to over two weeks depending on viral input. FTA cards were also shown to stabilize YFV RNA at high humidity if cards were desiccated prior to inoculation. These results support that FTA cards could be cost effective and easy to use in molecular diagnosis of YF, preserving viral RNA to allow for positive diagnoses in situations where maintaining cold-chain is not feasible.     

Kinetic and equilibrium studies of incorporation of di-sulfonated aluminum phthalocyanine into unilamellar vesicles.

The interactions of cis-di-sulfonated aluminum phthalocyanine (PcS(2)Al) with dimyristoylphosphatidylcholine (DMPC) unilamellar vesicles have been investigated by fluorescence spectroscopy. At pH 7.0, PcS(2)Al incorporates into the vesicles with a high affinity constant (2.7x10(6) M(-1), in terms of phospholipid concentration). The fluorescence changes following rapid mixing of PcS(2)Al with vesicles are biphasic. The first phase is attributed to the entry of PcS(2)Al into the vesicles, as deduced from the linear dependence of the rate upon lipid concentration. More surprisingly, this rate is strongly pH dependent with a marked maximum around pH 7.3, a result interpreted in terms of the coordination state of the aluminum ion in aqueous solutions. At this pH, a hydroxide ion neutralizes the residual positive charge of the metal ion that remains unbalanced after coordination by the phthalocyanine cycle. A water molecule is likely to complete the metal coordination sphere. Only this form, PcAl(+)(OH(-))(OH(2)), with an uncharged core is quickly incorporated into the vesicles. The protonation of OH(-) or the deprotonation of the coordinated H(2)O leading to a positively or negatively charged core, respectively, account for the observed pH effect. Studies on the effect of cholesterol addition and exchange of PcS(2)Al between vesicles and albumin all indicate the absence of transfer of the phthalocyanine between the vesicle hemileaflets, a result expected from the presence of the two negatively charged sulfonated groups at the ring periphery. Instead, the slower kinetic phase is likely due to the movement of the phthalocyanine becoming more buried within the outer leaflet upon the loss of the water molecule coordinated to the aluminum ion.     

Comparing Competitive Fitness of West Nile Virus Strains in Avian and Mosquito Hosts

Enzootic transmission of West Nile virus (WNV; Flaviviridae, Flavivirus) involves various species of birds and ornithophilic mosquitoes. Single nucleotide substitutions in the WNV genome may impact viral fitness necessary for WNV adaptation and evolution as previously shown for the WN02 genotype. In an effort to study phenotypic change, we developed an in vivo fitness competition model in two biologically relevant hosts for WNV. The House Finch (HOFI; Haemorhous mexicanus) and Culex tarsalis mosquitoes represent moderately susceptible hosts for WNV, are highly abundant in Western North America and frequently are infected with WNV in nature. Herein, we inoculated HOFIs and Cx. tarsalis competitively (dually) and singly with infectious-clone derived viruses of the founding California isolate COAV997-2003 (COAV997-IC), the founding North American isolate NY99 (NY99-IC), and a 2004 field isolate from California (CA-04), and compared the replicative capacities (fitness) of these viruses to a genetically marked virus of COAV997 (COAV997-5nt) by measuring RNA copy numbers. COAV997 and COAV997-5nt exhibited neutral fitness in HOFIs and Cx. tarsalis, and the temperature-sensitive phenotype of COAV997 did not affect replication in HOFIs as none of the infected birds became febrile. The NY99 and CA-04 isolates demonstrated elevated fitness in HOFIs compared to COAV997-5nt, whereas all viruses replicated to similar titers and RNA copies in Cx. tarsalis, and the only fitness differences were related to infection rates. Our data demonstrated that competitive replication allows for the sensitive comparison of fitness differences among two genetically closely related viruses using relevant hosts of WNV while eliminating host-to-host differences. In conclusion, our approach may be helpful in understanding the extent of phenotypic change in fitness associated with genetic changes in WNV.     

Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization

One of the challenges of genomic research after the completion of the human genome project is to assign a function to all the genes and to understand their interactions and organizations. Among the various techniques, the emergence of chromosome engineering tools with the aim to manipulate large genomic regions in the mouse model offers a powerful way to accelerate the discovery of gene functions and provides more mouse models to study normal and pathological developmental processes associated with aneuploidy. The combination of gene targeting in ES cells, recombinase technology, and other techniques makes it possible to generate new chromosomes carrying specific and defined deletions, duplications, inversions, and translocations that are accelerating functional analysis. This review presents the current status of chromosome engineering techniques and discusses the different applications as well as the implication of these new techniques in future research to better understand the function of chromosomal organization and structures.     

Exploring a new biodiversity frontier: subterranean ants in northern Australia

Although it is common for ant surveys to uncover previously uncollected species, a recent study of subterranean ants in Amazonian Ecuador has indicated that an entire ant fauna may remain largely undiscovered. Here we report on the first systematic investigation of subterranean ants in northern Australia, in order to assess the extent to which the high abundance and diversity of subterranean ants in Amazonia is apparent in tropical Australia. We use a novel sampling technique that combines elements of an attractant bait and a pitfall trap, and allows many traps to be deployed simultaneously. Our main study was conducted at three closely approximated sites in Darwin, where the local ant fauna has been intensively surveyed using conventional (above-ground) sampling techniques. The 720 traps deployed resulted in 421 species records, representing 29 species from 17 genera. Sixteen of these species have cryptobiotic morphology, with four recorded here for the first time. Remarkably, one of these four (a blind species of Solenopsis) was the second most frequently caught species in subterranean traps, with 70 records. Ant abundance, species richness and composition varied markedly between sites, despite site similarity in soils and vegetation. Total ant records were greater in the middle compared with start of the wet season, declined with depth, and were greater after 4 days than one. Sampling at six sites in the Mitchell Falls area of the northern Kimberley region, 1,200 km southwest of Darwin, also revealed several cryptobiotic species new to science, including a new genus record (Pseudolasius) for Western Australia. Our underground sampling has therefore revealed an abundant and diverse subterranean ant fauna in northern Australia, containing many cryptobiotic species not previously collected. We use our results to provide methodological guidelines for most effectively sampling this fauna. Combined with the Amazonian study, our findings indicate that a specialist subterranean ant fauna, including numerous species remaining to be discovered, might be a feature of tropical landscapes throughout the world.     

Plant infection by two different viruses induce contrasting changes of vectors fitness and behavior

Insect-vectored plant viruses can induce changes in plant phenotypes,thus influencing plant-vector interactions in a way that may promote their dispersal according to their mode of transmission (i.e.,circulative vs.noncirculative).This indirect vector manipulation requires host-virus-vector coevolution and would thus be effective solely in very specific plant-virus-vector species associations.Some studies suggest this manipulation may depend on multiple factors relative to various intrinsic characteristics of vectors such as transmission efficiency.In anintegrative study,we tested the effects of infection of the Brassicaceae Camelina sativa with the noncirculative Cauliflower mosaic virus (CaMV)or the circulative Turnip yellows virus (TuYV)on the host-plant colonization of two aphid species differing in their virus transmission efficiency:the polyphagous Myzus persicae,efficient vector of both viruses,and the Brassicaceae specialist Brevicoryne brassicae,poor vector of TuYV and efficient vector of CaMV.Results confirmed the important role of virus mode of transmission as plant-mediated effects of CaMV on the two aphid species induced negative alterations of feeding behavior (i.e.,decreased phloem sap ingestion)and performance that were both conducive for virus fitness by promoting dispersion after a rapid acquisition.In addition,virus transmission efficiency may also play a role in vector manipulation by viruses as only the responses of the efficient vector to plant-mediated effects of TuYV,that is,enhanced feeding behavior and performances,were favorable to their acquisition and further dispersal.Altogether,this work demonstrated that vector transmission efficiency also has to be considered when studying the mechanisms underlying vector manipulation by viruses.Our results also re- inforce the idea that vector manipulation requires coevolution between plant,virus and vector.