B.S. Weir publications
4.9K views | +1 today
Follow
B.S. Weir publications
My scientific publications
Curated by Bevan Weir
Your new post is loading...
Your new post is loading...
Scooped by Bevan Weir
Scoop.it!

First report of Rhizoctonia solani anastomosis group AG-4 HG-I in the Lao PDR

First report of Rhizoctonia solani anastomosis group AG-4 HG-I in the Lao PDR | B.S. Weir publications | Scoop.it

Rhizoctonia solani anastomosis group AG-4 HG-I is reported for the first time from the Lao PDR. It was isolated from gai lan (Brassica oleracea var. alboglabra) affected by collar rot, seedling death, root rot and stunting of older plants from the Paksong area of Champasak province. The anastomosis group was confirmed by sequencing and Koch’s postulates were fulfilled.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois | Weir | Phytotaxa

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in New Zealand, the other of coconut (Cocos nucifera) in Hawaii, poorly match the current species descriptions. To verify whether these isolates belong to separate species a detailed morphological study and phylogenetic analysis consisting of eight genetic loci was conducted. On the basis of genetic and morphological differences and host specificity, we present the formal description of two new species in Clade 5, Phytophthora agathidicida sp. nov. and Phytophthora cocois sp. nov. To clarify the typification of the other Clade 5 species, an authentic ex-holotype culture of Phytophthora castaneae is designated and P. heveae is lectotypified and epitypified.

 

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Phylogenetic relationships among global popul... [Phytopathology. 2012] - PubMed - NCBI

ABSTRACT Pseudomonas syringae pv. actinidiae, the causal agent of canker in kiwifruit (Actinidia spp.) vines, was first detected in Japan in 1984, followed by detections in Korea and Italy in the early 1990s. Isolates causing more severe disease symptoms have recently been detected in several countries with a wide global distribution, including Italy, New Zealand, and China. In order to characterize P. syringae pv. actinidiae populations globally, a representative set of 40 isolates from New Zealand, Italy, Japan, South Korea, Australia, and Chile were selected for extensive genetic analysis. Multilocus sequence analysis (MLSA) of housekeeping, type III effector and phytotoxin genes was used to elucidate the phylogenetic relationships between P. syringae pv. actinidiae isolates worldwide. Four additional isolates, including one from China, for which shotgun sequence of the whole genome was available, were included in phylogenetic analyses. It is shown that at least four P. syringae pv. actinidiae MLSA groups are present globally, and that marker sets with differing evolutionary trajectories (conserved housekeeping and rapidly evolving effector genes) readily differentiate all four groups. The MLSA group designated here as Psa3 is the strain causing secondary symptoms such as formation of cankers, production of exudates, and cane and shoot dieback on some kiwifruit orchards in Italy and New Zealand. It is shown that isolates from Chile also belong to this MLSA group. MLSA group Psa4, detected in isolates collected in New Zealand and Australia, has not been previously described. P. syringae pv. actinidiae has an extensive global distribution yet the isolates causing widespread losses to the kiwifruit industry can all be traced to a single MLSA group, Psa3.

 

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

The Colletotrichum gloeosporioides species complex

The Colletotrichum gloeosporioides species complex | B.S. Weir publications | Scoop.it

The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within C. gloeosporioides and its putative teleomorph Glomerella cingulata.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Mycotaxon: Characterisation and neotypification of Gloeosporium kaki Hori as Colletotrichum horii nom. nov.

Mycotaxon: Characterisation and neotypification of Gloeosporium kaki Hori as Colletotrichum horii nom. nov. | B.S. Weir publications | Scoop.it

A neotype is designated for the persimmon anthracnose pathogen Gloeosporium kaki Hori and the fungus is transferred to Colletotrichum as Colletotrichum horii nom. nov. Molecular and morphological analyses place this species as a distinct group within the Colletotrichum gloeosporioides sensu lato species complex. The fungus is associated with dieback and canker of twigs and young branches of persimmon, as well as spots on unripe fruit. The disease occurs on persimmon in China, Japan, and Korea, and is reported for the first time from New Zealand.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

IJSEM: ‘Candidatus Liberibacter solanacearum’, associated with plants in the family Solanaceae

IJSEM: ‘Candidatus Liberibacter solanacearum’, associated with plants in the family Solanaceae | B.S. Weir publications | Scoop.it

A liberibacter (isolate NZ082226) was detected in a symptomatic tomato plant and subsequently in five other members of the family Solanaceae: capsicum, potato, tamarillo, cape gooseberry and chilli. Phylogenetic analyses of the 16S rRNA gene sequence, the deduced amino acid sequence of the rplJ gene and a partial nucleotide sequence of the β operon indicated that isolate NZ082226 represents a novel candidate species of ‘Candidatus Liberibacter’, for which the name ‘Candidatus Liberibacter solanacearum’ is proposed.

 

International Journal of Systematic and Evolutionary Microbiology

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Applied and Environmental Microbiology: Unexpectedly Diverse Mesorhizobium Strains and Rhizobium leguminosarum Nodulate Native Legume Genera of New Zealand, while Introduced Legume Weeds Are Nodula...

Applied and Environmental Microbiology: Unexpectedly Diverse Mesorhizobium Strains and Rhizobium leguminosarum Nodulate Native Legume Genera of New Zealand, while Introduced Legume Weeds Are Nodula... | B.S. Weir publications | Scoop.it

The New Zealand native legume flora are represented by four genera, Sophora, Carmichaelia, Clianthus, and Montigena. The adventive flora of New Zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. Until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in New Zealand. The success of the introduced species may be due, at least in part, to the nature of their rhizobial symbioses. This study set out to address this issue by identifying rhizobial strains isolated from species of the four native legume genera and from the introduced weeds: Acacia spp. (wattles), Cytisus scoparius (broom), and Ulex europaeus (gorse). The identities of the isolates and their relationship to known rhizobia were established by comparative analysis of 16S ribosomal DNA, atpD, glnII, and recA gene sequences. Maximum-likelihood analysis of the resultant data partitioned the bacteria into three genera. Most isolates from native legumes aligned with the genus Mesorhizobium, either as members of named species or as putative novel species. The widespread distribution of strains from individual native legume genera across Mesorhizobium spp. contrasts with previous reports implying that bacterial species are specific to limited numbers of legume genera. In addition, four isolates were identified as Rhizobium leguminosarum. In contrast, all sequences from isolates from introduced weeds aligned with Bradyrhizobium species but formed clusters distinct from existing named species. These results show that native legume genera and these introduced legume genera do not have the same rhizobial populations.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Unravelling Colletotrichum species associated with Camellia: employing ApMat and GS loci to resolve species in the C. gloeosporioides complex

We investigated the phylogenetic diversity of 144 Colletotrichum isolates associated with symptomatic and asymptomatic tissues of Camellia sinensis and other Camellia spp. from seven provinces in China (Fujian, Guizhou, Henan, Jiangxi, Sichuan, Yunnan, Zhejiang), and seven isolates obtained from other countries, including Indonesia, UK, and the USA. Based on multi-locus (ACT, ApMat, CAL, GAPDH, GS, ITS, TUB2) phylogenetic analyses and phenotypic characters, 11 species were distinguished, including nine well-characterised species (C. alienum, C. boninense, C. camelliae, C. cliviae, C. fioriniae, C. fructicola, C. gloeosporioides, C. karstii, C. siamense), and two novel species (C. henanense and C. jiangxiense). Of these, C. camelliae proved to be the most dominant and probably host specific taxon occurring on Camellia. An epitype is also designated for the latter species in this study. Colletotrichum jiangxiense is shown to be phylogenetically closely related to the coffee berry pathogen C. kahawae subsp. kahawae. Pathogenicity tests and the pairwise homoplasy index test suggest that C. jiangxiense and C. kahawae subsp. kahawae are two independent species. This study represents the first report of C. alienum and C. cliviae occurring on Camellia sinensis. In addition, our study demonstrated that the combined use of the loci ApMat and GS in a phylogenetic analysis is able to resolve all currently accepted species in the C. gloeosporioides species complex.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Diverse Honeydew-Consuming Fungal Communities Associated with Scale Insects

Diverse Honeydew-Consuming Fungal Communities Associated with Scale Insects | B.S. Weir publications | Scoop.it

Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different “species” (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated with the keystone insect-honeydew systems of New Zealand’s native forests and suggests there is much to learn about sooty mould communities.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

The ApMat marker can resolve Colletotrichum species: a case study with Mangifera indica - Springer

Anthracnose disease caused by the Colletotrichum gloeosporioides species complex is a major problem worldwide. In this study, we investigated the phylogenetic diversity of 207 Indian Colletotrichum isolates, associated with symptomatic and asymptomatic tissues of mango, belonging to this species complex. Phylogenetic analyses were performed based on a 6-gene dataset (act, cal, chs1, gapdh, ITS and tub2), followed by ApMat sequence-analysis. The ApMat-based phylogeny was found to be superior as it provided finer resolution in most of the species-level clades. Importantly, the ApMat marker identified seven lineages within C. siamense sensu lato, including C. jasmini-sambac, C. hymenocallidis, C. melanocaulon, C. siamense sensu stricto and three undesignated, potentially novel lineages. In this study, C. fragariae sensu stricto, C. fructicola, C. jasmini-sambac, C. melanocaulon and five undesignated, potentially novel lineages were found to be associated with mango tissues. There is a need to develop a consensus among mycologists as to which genes should be used to define and delimit a Colletotrichum species and in the mean time mycologists should voluntarily restrain from describing new species based on inadequate datasets.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

PNAS: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

PNAS: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi | B.S. Weir publications | Scoop.it

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Australasian Plant Pathology: Three new Phaeoacremonium species on grapevines in New Zealand

Australasian Plant Pathology: Three new Phaeoacremonium species on grapevines in New Zealand | B.S. Weir publications | Scoop.it

Three new species of Phaeoacremonium (Pm.) found in discoloured wood of grapevine are described and named Pm. armeniacum, Pm. globosum and Pm. occidentale. Phaeomoniella chlamydospora was isolated from the same vines, but no other Phaeoacremonium spp. were present. Phaeoacremonium spp. have been associated with Petri and esca diseases in grapevine. In pathogenicity trials, the new Phaeoacremonium spp. consistently caused brown discolouration in the inoculated wood. All species caused mortality of cv. 101–14 rootstock cuttings, 22–60% of cuttings surviving 10 weeks after inoculation. Rootstock cv. 5C was less susceptible, with 80–100% of cuttings surviving. The three new species of Phaeoacremonium are genetically distinct from all those previously described and also show subtle morphological differences in the structure and size of the phialides and conidia. Phylogenetic analysis of β-tubulin and actin genes showed that the new species Pm. globosum and Pm. armeniacum are closely related to Pm. argentinense from Argentina, while Pm. occidentale is more closely related to Pm. mortoniae from vineyards in the northern hemisphere. The new species were isolated from rootstock imported into New Zealand ~25 years ago from California. They are not closely related to species known from grape in California, and no conclusion can be made about whether they were imported in the recent past on infected plants, or if they are indigenous to New Zealand. Many Phaeoacremonium species have a broad host range, and more intensive surveys of the native New Zealand flora and vineyards are needed before their origin can be determined.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

FEMS Microbiology Letters: Diversity of 16S rDNA sequences of Rhizobium spp. implications for species determinations

FEMS Microbiology Letters: Diversity of 16S rDNA sequences of Rhizobium spp. implications for species determinations | B.S. Weir publications | Scoop.it

Comparative analysis of 70 16S rDNA sequences representing 20 Rhizobium species (including pathogenic Agrobacterium spp.) was conducted using Maximum Likelihood to establish relationships of species using multiple sequences. There is no significant internal division of the Rhizobium clade to suggest that it represents more than one genus. Plant pathogenic (Agrobacterium) species are distributed within the genus. The analysis supported the synonymy of some species (Rhizobium gallicum and Rhizobium mongolense) and the need for comparative investigations of the tumorigenic and nodulating properties of Rhizobium tropici and Rhizobium rhizogenes. Misidentification of some sequences may conceal one or more putative novel species. Some sequences appear to be misidentified because of faulty sequencing or incomplete or inadequate analysis.

more...
No comment yet.
Scooped by Bevan Weir
Scoop.it!

Plant Disease: A New ‘Candidatus Liberibacter’ Species Associated with Diseases of Solanaceous Crops

Plant Disease: A New ‘Candidatus Liberibacter’ Species Associated with Diseases of Solanaceous Crops | B.S. Weir publications | Scoop.it

A new disease of glasshouse-grown tomato and pepper in New Zealand has resulted in plant decline and yield loss. Affected plants are characterized by spiky, chlorotic apical growth, curling or cupping of the leaves, and overall stunting. Transmission electron microscopy revealed the presence of phloem-limited bacterium-like organisms in symptomatic plants. The strategy used to identify the bacterium involved using specific prokaryote polymerase chain reaction (PCR) primers in combination with universal 16S rRNA primers. Sequence analysis of the 16S rRNA gene, the 16S/23S rRNA spacer region, and the rplKAJL-rpoBC operon revealed that the bacterium shared high identity with ‘Candidatus Liberibacter’ species. Phylogenetic analysis showed that the bacterium is distinct from the three citrus liberibacter species previously described and has been named ‘Candidatus Liberibacter solanacearum’. This is the first report of a liberibacter naturally infecting a host outside the Rutaceae family. A specific PCR primer pair was developed for its detection.

more...
No comment yet.