A recurrent mutation in the BMP type I receptor ACVR1 causes inherited and sporadic fibrodysplasia ossificans progressiva

Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disorder of skeletal malformations and progressive extraskeletal ossification. We mapped FOP to chromosome 2q23-24 by linkage analysis and identified an identical heterozygous mutation (617G→A; R206H) in the glycine-serine (GS) activation domain of ACVR1, a BMP type I receptor, in all affected individuals examined. Protein modeling predicts destabilization of the GS domain, consistent with constitutive activation of ACVR1 as the underlying cause of the ectopic chondrogenesis, osteogenesis and joint fusions seen in FOP.

Ceratocystis atrox sp. nov. associated with Phoracantha acanthocera infestations on Eucalyptus grandis in Australia

Ceratocystis spp. include important pathogens of trees as well as apparently saprophytic species. Four species have been recorded on Eucalyptus grandis in Australia, of which only one, C. pirilliformis Barnes and M.J. Wingf., is known to be pathogenic. A recent survey of pests and diseases of Eucalyptus trees in northern Queensland revealed a species of Ceratocystis associated with the tunnels made by the aggressive wood-boring insect Phoracantha acanthocera (Macleay) (Cerambicydae: Coleoptera). The aim of the present study was to identify the fungus based on morphological characteristics and comparisons of DNA sequence data for three gene regions. The fungus peripherally resembles C. fimbriata Ell. and Halst. but differs from this species most obviously by having much darker mycelium, longer ascomatal necks, segmented hyphae and an absence of aleuroconidia. Comparisons of combined sequence data confirmed that the Ceratocystis sp. from P. acanthocera represents an undescribed taxon, which is provided with the name Ceratocystis atrox sp. nov. C. atrox appears to have a close relationship with P. acanthocera, although its role in the biology of the insect is unknown and its pathogenicity has not been considered.

Diversity of methanogens in ruminants in Queensland

Methane emissions from ruminant livestock represent a loss of carbon during feed conversion, which has implications for both animal productivity and the environment because this gas is considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in different breeds of cattle and sheep, as well as in response to different diets, is required. A study was undertaken using the molecular techniques denaturing gradient gel electrophoresis, DNA cloning and DNA sequence analysis to define the extent of diversity among methanogens in ruminants, particularly Bos indicus cross cattle, on differing forages in Queensland. It was found that the diversity of methanogens in forage-fed cattle in Queensland was greater than in grain-fed cattle but there was little variability in methanogen community composition between cattle fed different forages. The species that dominate the rumen microbial communities of B. indicus cross cattle are from the genus Methanobrevibacter, although rumen-fluid inoculated digestors fed Leucaena leucocephala leaf were populated with Methanosphaera-like strains, with the Methanobrevibacter-like strains displaced. If ruminant methane emissions are to be reduced, then antimethanogen bioactives that target both broad groups of ruminant methanogens are most likely to be needed, and as a part of an integrated suite of approaches that redirect rumen fermentation towards other more useful end products.

Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations.

The fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis, is enigmatic because it occurs globally in both declining and apparently healthy (non-declining) amphibian populations. This distribution has fueled debate concerning whether, in sites where it has recently been found, the pathogen was introduced or is endemic. In this study, we addressed the molecular population genetics of a global collection of fungal strains from both declining and healthy amphibian populations using DNA sequence variation from 17 nuclear loci and a large fragment from the mitochondrial genome. We found a low rate of DNA polymorphism, with only two sequence alleles detected at each locus, but a high diversity of diploid genotypes. Half of the loci displayed an excess of heterozygous genotypes, consistent with a primarily clonal mode of reproduction. Despite the absence of obvious sex, genotypic diversity was high (44 unique genotypes out of 59 strains). We provide evidence that the observed genotypic variation can be generated by loss of heterozygosity through mitotic recombination. One strain isolated from a bullfrog possessed as much allelic diversity as the entire global sample, suggesting the current epidemic can be traced back to the outbreak of a single clonal lineage. These data are consistent with the current chytridiomycosis epidemic resulting from a novel pathogen undergoing a rapid and recent range expansion. The widespread occurrence of the same lineage in both healthy and declining populations suggests that the outcome of the disease is contingent on environmental factors and host resistance.

Austropleospora osteospermi gen. et sp nov and its host specificity and distribution on Chrysanthemoides monilifera ssp rotundata in Australia.

Hendersonia osteospermi was found for the first time in Australia on leaf spots of the introduced invasive plant Chrysanthemoides monilifera ssp. rotundata (bitou bush) in coastal regions of New South Wales. Pathogenicity tests on species from 11 tribes in the family Asteraceae, demonstrated that H. osteospermi caused severe necrosis on leaves and stems of C. monilifera ssp. rotundata and its congener C. monilifera ssp. monilifera (boneseed). Small necrotic spots also developed on Osteospermum fruticosum and Dimorphotheca cuneata in the Calenduleae and on Helianthus annuus (sunflower) in the Heliantheae. None of the other plant species tested developed leaf spots, although H. osteospermi was re-isolated from senescent leaves of Cynara scolymus (globe artichoke) in the Cynareae and Vernonia cinerea in the Vernonieae. Single ascospores from ascomata of a Pleospora-like fungus found on diseased stems of bitou bush produced H. osteospermi in culture, which proved the anamorph/teleomorph connection. The ITS region of both a single-ascospore isolate and a single-conidium isolate were sequenced and found to be identical. The taxonomic status of H. osteospermi is re-examined and Austropleospora osteospermi gen. et sp. nov. is described as its teleomorph based on morphology, host range tests and DNA sequence analysis. The potential of A. osteospermi for the biological control of bitou bush and boneseed in Australia is discussed.

Campylobacter jejuni and Campylobacter coli Genotyping by High-Resolution Melting Analysis of a flaA Fragment.

The highly variable flagellin-encoding flaA gene has long been used for genotyping Campylobacter jejuni and Campylobacter coli. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The objective of this study was to apply HRM analysis to flaA-based genotyping. The initial aim was to identify a suitable flaA fragment. It was found that the PCR primers commonly used to amplify the flaA short variable repeat (SVR) yielded a mixed PCR product unsuitable for HRM analysis. However, a PCR primer set composed of the upstream primer used to amplify the fragment used for flaA restriction fragment length polymorphism (RFLP) analysis and the downstream primer used for flaA SVR amplification generated a very pure PCR product, and this primer set was used for the remainder of the study. Eighty-seven C. jejuni and 15 C. coli isolates were analyzed by flaA HRM and also partial flaA sequencing. There were 47 flaA sequence variants, and all were resolved by HRM analysis. The isolates used had previously also been genotyped using single-nucleotide polymorphisms (SNPs), binary markers, CRISPR HRM, and flaA RFLP.flaA HRM analysis provided resolving power multiplicative to the SNPs, binary markers, and CRISPR HRM and largely concordant with the flaA RFLP. It was concluded that HRM analysis is a promising approach to genotyping based on highly variable genes.

Grey Mackerel (Scomberomorus semifasciatus) microsatellite genotypes (nine loci) representing twelve regions along Australia's northern coastline from the eastern coast of Queensland to the western coast of Western Australia.

Scomberomorus semifasciatus is an Australian endemic found in tropical, coastal waters from eastern to western Australia. Commercial and recreational exploitation is common and regulated by state-based authorities. This study used mitochondrial DNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from twelve, equidistant sampling locations. Samples (n=544) were genotyped with nine microsatellite loci, and 353 were sequenced for d-loop (384 bp) and ATP (800bp) mitochondrial DNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, northwest coast of the Northern Territory, Gulf of Carpentaria and the east coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the east coast of Queensland was high, but in contrast, there was a clear genetic break between populations in Western Australia compared to the rest of northern Australia. This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (northwestern Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that the Gulf of Carpentaria stock should be co-managed by authorities in Queensland and Northern Territory.

Outbreak of angular leaf spot, caused by Xanthomonas fragariae, in a Queensland strawberry germplasm collection.

Strawberry (Fragaria (x) ananassa) plants exhibiting leaf lesions consistent with angular leaf spot (ALS, caused by Xanthomonas fragariae Kennedy and King 1962) were identified in the Queensland strawberry germplasm at Bundeberg in May 2010. Water suspensions of bacterial ooze tested positive using a previously described primer set. However, the slow growth rate of X. fragariae and the presence of a fast-growing, non-pathogenic, undescribed Xanthomonas species presented problems that were overcome by dilution plating and DNA sequence analysis. Sequencing of the gyrB locus of putative colonies of X. fragariae indicated 100% sequence similarity to other X. fragariae isolates. A new set of diagnostic primers for X. fragariae based on the gyrB locus is presented.

Teratosphaeria pseudoeucalypti, new cryptic species responsible for leaf blight of Eucalyptus in subtropical and tropical Australia

Sub-tropical and tropical plantations of Eucalyptus grandis hybrids in eastern Australia have been severely affected by anamorphs of Teratosphaeria (formerly Kirramyces) causing a serious leaf blight disease. Initially the causal organism in Queensland, Australia, was identified as Teratosphaeria eucalypti, a known leaf parasite of endemic Eucalyptus spp. However, some inconsistencies in symptoms, damage and host range suggested that the pathogen in Queensland may be a new species. Isolates of T. eucalypti from throughout its known endemic range, including Queensland and New Zealand, where it is an exotic pathogen, were compared using multiple gene phylogenies. Phylogenetic studies revealed that the species responsible for leaf blight in Queensland represents a new taxon, described here as Teratosphaeria pseudoeucalypti. While the DNA sequence of T. pseudoeucalypti was more similar to T. eucalypti, the symptoms and cultural characteristics resembled that of T. destructans. The impact of this disease in central Queensland has increased annually and is the major threat to the eucalypt plantation industry in the region.

The application of DArTseq technology to pineapple

DArTseq technology is potentially the most appropriate system to discover hundreds of polymorphic genomic loci, scoring thousands of unique genomic-wide DNA fragments in one single experiment, without requiring existing DNA sequence information. The DArT complexity reduction approach in combination with Illumina short read sequencing (Hiseq2000) was applied. To test the application of DArTseq technology in pineapple, a reference population of 13 Ananas genotypes from primitive wild accessions to modern cultivars was used. In a comparison of 3 systems, the combination of restriction enzymes PstI and MseI performed the best producing 18,900 DArT markers and close to 20,000 SNPs. Based on these markers genetic relationships between the samples were identified and a dendrogram was generated. The topography of the tree corresponds with our understanding of the genetic relationships between the genotypes. Importantly, the replicated samples of all genotypes have a dissimilarity of close to 0.0 and occupy the same positions on the tree, confirming high reproducibility of the markers detected. Eventually it is planned that molecular markers will be identified that are associated with resistance to Phytophthora cinnamomi (Pc), the most economically important pathogen of pineapple in Australia, as genetic resistance is known to exist within the Ananas. Marker assisted selection can then be utilized in a pineapple breeding program to develop cultivars resistant to Pc.

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species.

The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are believed to represent novel species. Diaporthe gulyae sp. nov. is described for isolates that caused a severe stem canker, specifically pale brown to dark brown, irregularly shaped lesions centred at the stem nodes with pith deterioration and mid-stem lodging. This pathogenicity of D. gulyae was confirmed by satisfying Koch's Postulates. These symptoms are almost identical to those of sunflower stem canker caused by D. helianthi that can cause yield reductions of up to 40% in Europe and the USA, although it has not been found in Australia. We show that there has been broad misapplication of the name D. helianthi to many isolates of Diaporthe ( Phomopsis) found causing, or associated with, stem cankers on sunflower. In GenBank, a number of isolates had been identified as D. helianthi, which were accommodated in several clades by molecular phylogenetic analysis. Two less damaging species, D. kochmanii sp. nov. and D. kongii sp. nov., are also described from cankers on sunflower in Australia.

Is Human-X Chromosome Inactivation A Sex-Determining Device

The evolutionary function of X chromosome inactivation is thought to be dosage compensation. However, there is, at present, little evidence to suggest that most X chromosome-linked genes require such compensation. Another view--that X chromosome inactivation may be related to sex determination--is examined here. Consider a hypothetical DNA sequence regulating a major structural gene concerned with the determination of maleness. If this regulatory sequence occurs in both X and Y chromosomes and if its copy number in the Y chromosome is significantly greater than in the X chromosome, then the male-determining properties of the Y chromosome could be attributed to this higher copy number. On the other hand, if the Y chromosome has the same copy number of this sequence as the X chromosome, it is difficult to see how determination of two sexes would occur under such circumstances because XX and XY genomes would then be indistinguishable in this regard. Such a situation seems to occur in the human species with respect to the banded krait minor satellite, a repetitious DNA sequence associated with sex determination. This apparent difficulty may be resolved if X chromosome inactivation renders regulatory as well as structural genes nonfunctional and thereby brings about a significant reduction in the effective copy number of X chromosome-linked DNA sequences concerned with sex determination. It is suggested that X chromosome inactivation brings about, in this manner, a critical inequality between XX and XY embryos and that sex determination in humans is a consequence of this inequality. An analogous situation appears to exist in certain insects in which inactivation of a haploid set of chromosomes (and presumably, therefore, a 50% reduction in the effective copy number of most genes) is associated with maleness. If this line of reasoning is correct, it would suggest that sex determination may be the primary function of X chromosome inactivation.

Phyllosticta spp. on cultivated Citrus in Australia

The occurrence of pathogenic and endophytic species of Phyllosticta on cultivated Citrus in Australia was investigated by DNA sequence analysis of specimens held in plant pathology herbaria and culture collections. Sequences of the internal transcribed spacer region (ITS1, 5.8S, ITS2), and partial translation elongation factor 1-alpha (TEF) gene of 41 Phyllosticta-like isolates from Citrus were compared to those sequences from the type specimens of Phyllosticta recorded from around the world. Phylogenetic analysis resolved all the sequences of Australian accessions into two major clades. One clade corresponded to P. citricarpa, which causes citrus black spot disease. The other clade contained P. capitalensis, which is a known endophyte of Citrus and many other plant species. All included herbarium accessions previously designated as Guignardia mangiferae are now designated P. capitalensis. No Australian isolates were identified as the newly described pathogens of citrus P. citriasiana or P. citrichinaensis, or the endophytes Guignarida mangiferae, P. brazilianiae, or P. citribraziliensis. © 2013 Australasian Plant Pathology Society Inc.

Molecular phylogenetic analysis reveals six new species of Diaporthe from Australia

Six new species of Diaporthe, D. beilharziae on Indigofera australis, D. fraxini-angustifoliae on Fraxinus angustifolia subsp. oxycarpa, D. litchicola on Litchi chinensis, D. nothofagi on Nothofagus cunninghamii, D. pascoei on Persea americana and D. salicicola on Salix purpurea from Australia are described and illustrated based on morphological characteristics and molecular analyses. Three of the new species no longer produced sporulating structures in culture and two of these were morphologically described from voucher specimens. Phylogenetic relationships of the new species with other Diaporthe species are revealed by DNA sequence analyses based on the internal transcribed spacer (ITS) region, and partial regions of the β-tubulin (BT) and translation elongation factor 1-alpha (TEF). © 2013 Mushroom Research Foundation.