A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria.

Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.

Cytopathological and histopathological diagnosis of canine splenic disorders.

OBJECTIVES: To determine (1) the common types of canine splenic disorders, and the breeds affected, that are diagnosed by cytopathological and histopathological examination in Sydney, Australia and (2) the accuracy of cytopathological examination compared with histopathological examination for the diagnosis of canine splenic disorders. DESIGN: 69 cytopathological and 51 histopathological diagnoses of canine splenic disorders presented to the Veterinary Pathology Diagnostic Services, The University of Sydney during 2006 and 2007 were tabulated and analysed; 17 cases examined both cytopathologically and histopathologically during 2001-07 were also analysed. RESULTS: The most common cytopathological diagnoses were benign disorders of growth, vascular disturbances and necrosis (29%), followed by no abnormalities detectable (28%), malignant neoplasms (20%), equivocal diagnoses (20%) and inflammatory disorders (3%). The most common breeds were Kelpie crosses and mixed breeds. The most common histopathological diagnoses were benign disorders of growth, vascular disturbances and necrosis (49%), followed by malignant neoplasms (43%) and inflammatory disorders (8%). The most common breeds were German Shepherd Dogs, Boxers and Maltese Terriers. Cytopathological and histopathological diagnoses were in complete agreement in 59% of cases, partial agreement in 29% and disagreement in 12%. CONCLUSION: Benign disorders of growth, vascular disturbances and necrosis were the most commonly diagnosed canine splenic disorders, both cytopathologically and histopathologically. Kelpie crosses presented most frequently for cytopathological examination. German Shepherd Dogs were the most common breed diagnosed histopathologically with haemangiosarcoma. Although cytopathological and histopathological splenic examinations are complementary for diagnosis, this study has shown a high correlation for complete and partial agreement between the two.

Molecular identification and phylogeny of Armillaria isolates from South America and Indo-Malaysia.

Armillaria root rot is a serious disease, chiefly of woody plants, caused by many species of Armillaria that occur in temperate, tropical and subtropical regions of the world. Very little is known about Armillaria in South America and Southeast Asia, although Armillaria root rot is well known in these areas. In this study, we consider previously unidentified isolates collected from trees with symptoms of Armillaria root rot in Chile, Indonesia and Malaysia. In addition, isolates from basidiocarps resembling A. novae-zelandiae and A. limonea, originating from Chile and Argentina, respectively, were included in this study because their true identity has been uncertain. All isolates in this study were compared, based on their similarity in ITS sequences with previously sequenced Armillaria species, and their phylogenetic relationship with species from the Southern Hemisphere was considered. ITS sequence data for Armillaria also were compared with those available at GenBank. Parsimony and distance analyses were conducted to determine the phylogenetic relationships between the unknown isolates and the species that showed high ITS sequence similarity. In addition, IGS-1 sequence data were obtained for some of the species to validate the trees obtained from the ITS data set. Results of this study showed that the ITS sequences of the isolates obtained from basidiocarps resembling A. novae-zelandiae are most similar to those for this species. ITS sequences for isolates from Indonesia and Malaysia had the highest similarity to A. novae-zelandiae but were phylogenetically separated from this species. Isolates from Chile, for which basidiocarps were not found, were similar in their ITS and IGS-1 sequences to the isolate from Argentina that resembled A. limonea. These isolates, however, had the highest ITS and IGS-1 sequence similarity to authentic isolates of A. luteobubalina and were phylogenetically more closely related to this species than to A. limonea.

Time-harmonic torsional waves in a composite cylinder with an imperfect interface

In this paper, the propagation of time-harmonic torsional waves in composite elastic cylinders is investigated. An imperfect interface is considered where tractions are continuous across the interface and the displacement jump is proportional to the stress acting on the interface. A frequency equation is derived for the rod and dispersion curves of normalized frequency as a function of normalized wave number for elastic bimaterials with varying values for the interface constant F are presented. The analysis is shown to recover the dispersion curves for a bimaterial rod with a perfect (welded) interface (F = 0), and has the correct limiting behavior for large F. It is shown that the modes, at any given frequency, are orthogonal, and it is outlined how the problem of reflection of a torsional mode by a planar defect (such as a circumferential crack) can be treated.