The rusts on Goodeniaceae and Stylidiaceae

Systematic relationships between the rusts on Goodeniaceae and Stylidiaceae were examined using phylogenetic analyses with two loci (internal transcribed spacer, large subunit region) from ribosomal DNA. Fresh specimens and herbarium material of four rust species (Puccinia dampierae, P. gilgiana, P. saccardoi and Uromyces scaevolae) from the Goodeniaceae and one (P. stylidii) from the Stylidiaceae were examined. A further species (P. lagenophorae) that is reported from hosts in Goodeniaceae and Asteraceae was included in our analysis. Our phylogenetic analysis recovered the rusts on Goodeniaceae and Stylidiaceae in clades sister to P. lagenophorae on Asteraceae. This supported a taxonomy in which P. lagenophorae is restricted to Asteraceae. Descriptions or taxonomic notes are provided for all of the known rusts on Goodeniaceae and Stylidiaceae.

Curvularia tsudae comb. nov. et nom. nov., formerly Pseudocochliobolus australiensis, and a revised synonymy for Curvularia australiensis

Cultures originally identified as Drechslera australiensis, from seeds of Chloris gayana in Japan, were the basis for Tsuda and Ueyama's new combination, Bipolaris australiensis, and its associated sexual morph Pseudocochliobolus australiensis. By studying ex-type materials of both Drechslera australiensis, which was originally isolated from seeds of Oryza sativa in Australia, and Pseudocochliobolus australiensis, we show by morphological and molecular phylogenetic analysis that these two specimens represent different species. Taxonomic confusion is resolved by the transfer of Pseudocochliobolus australiensis to Curvularia tsudae comb. nov. et nom. nov., together with a revised synonymy for Curvularia australiensis.

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three nonrecombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

Uromycladium falcatarium sp. nov., the cause of gall rust on Paraserianthes falcataria in south-east Asia

The gall rusts on Acacia spp. and Paraserianthes falcataria are caused by species of Uromycladium. Morphology and a phylogenetic analysis of four loci from ribosomal (SSU, ITS, LSU) and mitochondrial (CO3) DNA, showed that the rust on P. falcataria differed from U. tepperianum. Uromycladium falcatarium sp. nov. is described to accommodate this taxon, which can be differentiated from other species of Uromycladium by teliospore wall morphology, host genus and DNA sequence data.

Three new species of Tilletia on Eriachne from north-western Australia

Three new species of Tilletia are described from species of Eriachne (Poaceae) in the arid tropics of north-western Australia. In Western Australia, T. mactaggartii sp. nov. infects E. burkittii, and T. geeringii sp. nov. infects E. festucacea. Tilletia marjaniae sp. nov. infects E. pulchella subsp. dominii in Western Australia and the Northern Territory. These species are the first records of Tilletia on Eriachne. Phylogenetic relationships of these species were inferred from internal transcribed spacer of ribosomal RNA region and large subunit ribosomal RNA gene sequences.

Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

Summary We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses.

Human-associated fluoroquinolone-resistant Escherichia coli clonal lineages, including ST354, isolated from canine feces and extraintestinal infections in Australia

Phylogenetic group D extraintestinal pathogenic Escherichia coli (ExPEC), including O15:K52:H1 and clonal group A, have spread globally and become fluoroquinolone-resistant. Here we investigated the role of canine feces as a reservoir of these (and other) human-associated ExPEC and their potential as canine pathogens. We characterized and compared fluoroquinolone-resistant E. coli isolates originally identified as phylogenetic group D from either the feces of hospitalized dogs (n = 67; 14 dogs) or extraintestinal infections (n = 53; 33 dogs). Isolates underwent phylogenetic grouping, random amplified polymorphic DNA (RAPD) analysis, virulence genotyping, resistance genotyping, human-associated ExPEC O-typing, and multi-locus sequence typing. Five of seven human-associated sequence types (STs) exhibited ExPEC-associated O-types, and appeared in separate RAPD clusters. The largest subgroup (16 fecal, 26 clinical isolates) were ST354 (phylogroup F) isolates. ST420 (phylogroup B2); O1-ST38, O15:K52:H1-ST393, and O15:K1-ST130 (phylogroup D); and O7-ST457, and O1-ST648 (phylogroup F) were also identified. Three ST-specific RAPD sub-clusters (ST354, ST393, and ST457) contained closely related isolates from both fecal or clinical sources. Genes encoding CTX-M and AmpC β-lactamases were identified in isolates from five STs. Major human-associated fluoroquinolone-resistant ± extended-spectrum cephalosporin-resistant ExPEC of public health importance may be carried in dog feces and cause extraintestinal infections in some dogs.

Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish

Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr : Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L–1) of the freshwater resulted in the Sr : Ca being substantially higher than the marine water. Importantly, the otolith Sr : Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr : Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr : Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element : Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr : Ca alone can be problematic without an understanding of water chemistry.

Joint Regression and Association Models for Repeated Categorical Responses

The focus of this study is on statistical analysis of categorical responses, where the response values are dependent of each other. The most typical example of this kind of dependence is when repeated responses have been obtained from the same study unit. For example, in Paper I, the response of interest is the pneumococcal nasopharengyal carriage (yes/no) on 329 children. For each child, the carriage is measured nine times during the first 18 months of life, and thus repeated respones on each child cannot be assumed independent of each other. In the case of the above example, the interest typically lies in the carriage prevalence, and whether different risk factors affect the prevalence. Regression analysis is the established method for studying the effects of risk factors. In order to make correct inferences from the regression model, the associations between repeated responses need to be taken into account. The analysis of repeated categorical responses typically focus on regression modelling. However, further insights can also be gained by investigating the structure of the association. The central theme in this study is on the development of joint regression and association models. The analysis of repeated, or otherwise clustered, categorical responses is computationally difficult. Likelihood-based inference is often feasible only when the number of repeated responses for each study unit is small. In Paper IV, an algorithm is presented, which substantially facilitates maximum likelihood fitting, especially when the number of repeated responses increase. In addition, a notable result arising from this work is the freely available software for likelihood-based estimation of clustered categorical responses.

Novel Pathotypes of Elsinoe australis Associated with Citrus australasica and Simmondsia chinensis in Australia

Molecular phylogenetic analysis, morphology and pathogenicity to citrus fruit were used to study two isolates of Elsinoe australis associated with scab-like symptoms on a fruit of Citrus australasica (finger lime) and Simmondsia chinensis (jojoba) in Australia. In addition to being associated with finger lime, the isolate from finger lime could cause scab symptoms on C. x aurantium cv. Murcott tangor in pathogenicity tests, but could not cause scab symptoms on the other orange, mandarin, lemon or grapefruit tested. Pathogenicity tests also support previous studies showing the isolate from jojoba could not produce symptoms on fruit of C. natsudaidai. Based on the findings of this study, two novel pathotypes of E. australis are designated from Australia; namely the Finger Lime (FL) pathotype associated with finger lime, and the Jojoba Black Scab (JBS) pathotype associated with black scab of jojoba. The significance of these novel E. australis pathotypes on market access and biosecurity issues for citrus are briefly discussed.

Polyphasic characterization of four new plant pathogenic Phyllosticta species from China, Japan, and the United States

The black rot disease of Vitis species and other host genera of Vitacease is caused by Phyllosticta ampelicida and allied taxa which is considered to be a species complex. In this paper, we introduce four new species of Phyllosticta, including two from the P. ampelicida complex, based on a polyphasic characterization including disease symptoms and host association, morphology, and molecular phylogeny. The phylogenetic analysis was conducted based on the ribosomal internal transcribed spacer (ITS) region and a combined multi-locus alignment of the ITS, actin (ACT), partial translation elongation factor 1-alpha (TEF-1), and glyceraldehydes 3-phosphate dehydrogenase (GPDH) gene regions. Our study confirms the phylogenetic distinctions of the four new species, as well as their phenotypic differences with known species in the genus.

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas

Divergent genetic selection for wool growth as a single trait has led to major changes in sheep physiology and metabolism, including variations in rumen microbial protein production and uptake of α-amino nitrogen in portal blood. This study was conducted to determine if sheep with different genetic merit for wool growth exhibit distinct rumen bacterial diversity. Eighteen Merino wethers were separated into groups of contrasting genetic merit for clean fleece weight (CFW; low: WG− and high: WG+) and fed a blend of oaten and lucerne chaff diet at two levels of intake (LOI; 1 or 1.5 times maintenance energy requirements) for two seven-week periods in a crossover design. Bacterial diversity in rumen fluid collected by esophageal intubation was characterized using 454 amplicon pyrosequencing of the V3/V4 regions of the 16S rRNA gene. Bacterial diversity estimated by Phylogenetic distance, Chao1 and observed species did not differ significantly with CFW or LOI; however, the Shannon diversity index differed (P=0.04) between WG+ (7.67) and WG− sheep (8.02). WG+ animals had a higher (P=0.03) proportion of Bacteroidetes (71.9% vs 66.5%) and a lower (P=0.04) proportion of Firmicutes (26.6% vs 31.6%) than WG− animals. Twenty-four specific operational taxonomic units (OTUs), belonging to the Firmicutes and Bacteroidetes phyla, were shared among all the samples, whereas specific OTUs varied significantly in presence/abundance (P<0.05) between wool genotypes and 50 varied (P<0.05) with LOI. It appears that genetic selection for fleece weight is associated with differences in rumen bacterial diversity that persist across different feeding levels. Moderate correlations between seven continuous traits, such as methane production or microbial protein production, and the presence and abundance of 17 OTUs were found, indicating scope for targeted modification of the microbiome to improve the energetic efficiency of rumen microbial synthesis and reduce the greenhouse gas footprint of ruminants.

Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties

Background: Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles. Results: A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316bp. Variety IW had the highest SNP frequency (one SNP every 258bp) while KP and NDM had similar frequencies (one SNP every 369bp and 360bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3'-hydroxylase (F3'H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties. Conclusions: The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango. © 2015 Hoang et al.

Pythiogeton ramosum, a new pathogen of soft rot disease of ginger (Zingiber officinale) at high temperatures in Australia

Pythium soft rot (PSR) of ginger caused by a number of Pythium species is of the most concern worldwide. In Australia, PSR outbreaks associated with Pythium myriotylum was recorded in 2007. Our recent pathogenicity tests in Petri dishes conducted on ginger rhizomes and pot trials on ginger plants showed that Pythiogeton (Py.) ramosum, an uncommon studied oomycete in Pythiaceae, was also pathogenic to ginger at high temperature (30–35 °C). Ginger sticks excised from the rhizomes were colonised by Py. ramosum which caused soft rot and browning lesions. Ginger plants inoculated with Py. ramosum showed initial symptoms of wilting and leave yellowing, which were indistinguishable from those of Pythium soft rot of ginger, at 10 days after inoculation. In addition, morphological and phylogenetic studies indicated that isolates of Py. ramosum were quite variable and our isolates obtained from soft rot ginger were divided into two groups based on these variations. This is also for the first time Py. ramosum is reported as a pathogen on ginger at high temperatures.

Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews

So far 19 genera of downy mildews have been described, of which seven are parasitic to grasses. Here, we introduce a new genus, Baobabopsis, to accommodate two distinctive downy mildews, B. donbarrettii sp. nov., collected on Perotis rara in northern Australia, and B. enneapogonis sp. nov., collected on Enneapogon spp. in western and central Australia. Baobabopsis donbarrettii produced both oospores and sporangiospores that are morphologically distinct from other downy mildews on grasses. Molecular phylogenetic analyses showed that the two species of Baobabopsis occupied an isolated position among the known genera of graminicolous downy mildews. The importance of the Poaceae for the evolution of downy mildews is highlighted by the observation that more than a third of the known genera of downy mildews occur on grasses, while more than 90 % of the known species of downy mildews infect eudicots.