Duckchul Park

Manaaki Whenua - Landcare Research · Systematics Team

During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyp...

During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyp...

The impact of myrtle rust on the New Zealand landscape will include changes to the wider biotic communities associated with the rust’s hosts. These include fungi, contributors not only to disease but also nutrient cycling. If myrtle rust impacts diversity of nutrient cycling communities, then its effect will extend far beyond disease on its primary...

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. Hymenotorrendiella species are often assumed to be saprobic, their fruiting bodies developing on fallen leaves and dead wood but, in many cases,...

Cyttaria is a morphologically and biologically distinct genus comprising wood-inhabiting species that are biotrophic associates of trees in the genera Nothofagus sensu stricto and Lophozonia in southern South America, Australia, and New Zealand. The uniqueness of the fruit bodies and habitat of Cyttaria has led taxonomists to justify its placement...

There is a real and urgent need for new antibiotics able to kill Mycobacteria, acid-fast bacilli capable of causing multiple deadly diseases. These include members of the Mycobacterium tuberculosis complex, which causes the lung disease tuberculosis (TB) as well as non-tuberculous Mycobacteria (NTM) a growing cause of lung, skin, soft tissue, and o...

A second genus in Chlorociboriaceae is described here as Brahmaculus gen. nov. Macroscopically distinctive, all species have bright yellow apothecia with several apothecial cups held on short branches at the tip of a long stipe. The genus is widely distributed across the Southern Hemisphere; the four new species described here include two from Chil...

Modicella is an unusual genus within the Mortierellaceae because it forms relatively large terrestrial sporocarps. The two existing described species are rarely encountered. We describe a new species, M. albostipitata, from New Zealand in the southern hemisphere, which is both morphologically and phylogenetically distinct from the described species...

The Chatham Islands support several endemic species of scurvy grass (Lepidium), which are under threat of extinction. The species are affected by a pathogenic white blister rust (Albugo). The identity and origin of the pathogen are uncertain.The objectives were to determine the identity of the white rust affecting indigenous Lepidium species on the...

Sphaeropezia leucocheila is described as a new species from New Zealand. Known from a single specimen, its fruiting bodies were consistently associated with a patch of dead and dying leaves in a liverwort colony that included several species of Lepidoziaceae. A phylogenetic analysis places this fungus in Sphaeropezia, a genus that includes several...

A leaf-spotting fungus common on Phormium tenax in New Zealand is described here as Marthamyces harakeke sp. nov. The phylogenetic analysis prepared for the description of this new species showed Marthamyces to be polyphyletic. To resolve this, three Marthamyces species from Australia and New Zealand, M. barbatus , M. dracophylli , and M. gilvus ,...

A leaf-spotting fungal pathogen common on Metrosideros excelsa in New Zealand is described here as Blastacervulus metrosideri sp. nov. It has previously been identified in the New Zealand literature as Leptomelanconium sp. and as Staninwardia breviuscula. The choice of genus for this new species is supported by a phylogeny based on ITS and LSU sequ...

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such...

A section-based taxonomy of Cortinarius, covering large parts of the temperate North and South Hemispheres, is presented. Thirty-seven previously described sections are reviewed, while another forty-two sections are proposed as new or as new combinations. Twenty additional clades are recovered but not formally described. Furthermore, six new or com...

Animal reproductive proteins, especially those in the seminal fluid, have been shown to have higher levels of divergence than non-reproductive proteins and are often evolving adaptively. Seminal fluid proteins have been implicated in the formation of reproductive barriers between diverging lineages, and hence represent interesting candidates underl...

Contigs identified in the reproductive protein search. (XLSX)

Top-Hit species distribution for tblastx results for A) Hemideina thoracica and B) Hemideina crassidens. (PDF)

Gene ontology categories identified in the reproductive gene screen for A) Hemideina thoracica and B) Hemideina crassidens. (PDF)

Sample collection details. **Samples used for 454 sequencing. (XLSX)

Likelihood values and parameter estimates for site-specific models for each gene. Parameters in brackets are not free, and therefore are not counted when considering difference in the number of parameters for nested model comparisons. (XLSX)

McDonald Kreitman test results for each gene. a Yates correction is applied to G tests. (XLSX)

Primer sequences for candidate genes. Annotations from tblastx against non-redundant database. (XLSX)

Orthologous contigs pairs identified in the bidirectional tblastx search. (XLSX)

Sites identified as putatively under selection and their posterior probabilities under the M3 and M8 models. a Amino acid site in the original alignment, including gaps; BEB, Bayes Empirical Bayes posterior probability; NEB, Naïve Empirical Bayes; **Probability > 99%. (XLSX)

Deinacrida fallai and D. mahoenui orthologues identified from an unpublished de novo assembled illumina transcriptome data. (FASTA)

High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gr...

Botrytis populations in vineyards often show seasonal differences. Early season populations tend to be less pathogenic than those at harvest. This change probably reflects differences in competitive ability in winter versus summer conditions. Such a seasonal pattern was observed in a Waipara vineyard from 2008 to 2012. The population at owering was...

The phylogenetic classification of the species Burkholderia andropogonis within the Burkholderia genus was reassessed using 16S rRNA gene phylogenetic analysis and multilocus sequence analysis (MLSA). Both phylogenetic trees revealed two main groups, named A and B, strongly supported by high bootstrap values (100%). Group A encompassed all of the B...

Fungal taxonomy and classification, and fungal identification tools, are increasingly based on DNA sequencing technologies. In contrast, many historical records of fungi are based on morphologically identified specimens. Scientific collections of specimens or living cultures provide a resource to enable these early records to be genetically validat...

The status of the genus Tricholomopsis (Agaricales) in New Zealand is reviewed. T. rutilans is a species described from the northern hemisphere and recorded from plantations of exotic Pinus radiata in New Zealand. Historical collections identified as T. rutilans were subjected to morphological and phylogenetic analysis. The results show that most o...

The status of the genus Tricholomopsis (Agaricales) in New Zealand is reviewed. T. rutilans is a species described from the northern hemisphere and recorded from plantations of exotic Pinus radiata in New Zealand. Historical collections identified as T. rutilans were subjected to morphological and phylogenetic analysis. The results show that most o...

Ralstonia pseudosolanacearum is reported for the first time from the Lao PDR. Typical symptoms of wilt and vascular exudate were observed in potatoes and tomatoes in Paksong district, Champasak province. Pathogenicity was proven and identification was based on symptoms, commercial diagnostic test kits and sequence of the egl gene.

Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circo...

Neocoleroa metrosideri is described as a new species and phylogenetically it is shown to belong in the Sympoventuriaceae, a recently established family, sister to the Venturiaceae. No other sequences are available for Neocoleroa but this new species is morphologically typical of the type species, with distinctive lobed to dichotomously branched, bl...

A xylariaceous fungus on the dead leaves of Phormium tenax and P. cookianum is described as a new genus and species, Entalbostroma erumpens. Phylogenetically E. erumpens is close to Xylaria amphithele. The sexual state resembles Kretzschmariella in general morphology, but the two genera are phylogenetically distant. The asexual state can be used to...

Diseases caused by Botrytis spp. are one of the major management issues in New Zealand vineyards. These fungi are genetically diverse across New Zealand's vineyards, with this diversity being reflected in differences in pathogenicity and fungicide resistance between populations. These populations are known to differ in their seasonal and regional d...

Background There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along...

Arbuscular mycorrhizal fungi (AMF) are components of coastal dune ecosystems around the globe where they provide a range of benefits to plants. The diversity and structure of AMF communities within these ecosystems, however, are poorly known. This study presents the first report of an AMF community in a New Zealand dune. Root samples were collected...

A cleistothecial fungus, known only from the shells of giant land snails of the family Rhytidae, is described as a new genus and species within Onygenales, Harorepupu aotearoa gen. sp. nov. Known only from the sexual morph, this fungus is characterized morphologically by a membranous ascoma with no appendages and ascospores with a sparse network of...

Here, we report the draft genome sequence of Burkholderia andropogonis ICMP2807, a phytopathogenic bacterium isolated from Sorghum bicolor plants in the United States. FOOTNOTES Address correspondence to Suzete Aparecida Lanza Destéfanoa, suzete{at}biologico.sp.gov.br. Citation Lopes-Santos L, Castro DBA, Ottoboni LMM, Park D, Weir BS, Destéfano SA...

The asexual form of the grape powdery mildew, Erysiphe necator, has been present in New Zealand for over 100 years. In 2013 the sexual stage was reported for the first time in vineyards in Hawke’s Bay associated with increased disease issues. This paper presents an initial genetic analysis of New Zealand populations compared to known populations ov...

The discovery of Chlorovibrissea chilensis sp. nov. expands the distribution of Chlorovibrissea from Australasia to include South America. C. chilensis, phylogenetically distinct from other species in the genus, is also characterized morphologically by its ascoma with emerald green stalk and pale orange-brown head, budding paraphyses and 5-6-septat...

Morphological and phylogenetic data are used to revise the genus Torrendiella. The type species, described from Europe, is retained within the Rutstroemiaceae. However, Torrendiella species reported from Australasia, southern South America and China were found to be phylogenetically distinct and have been recombined in the newly proposed genus Hyme...

Species- and population-specific differences in fungicide resistance and aggressiveness within Botrytis makes basic data on genetic diversity important for understanding disease caused by this fungus. Genetic diversity of Botrytis was surveyed between 2008 and 2012 from grapes from five New Zealand wine-growing regions. A total of 1226 isolates wer...

Grape powdery mildew first reported in New Zealand in 1901 is widespread in New Zealand grape growing regions causing significant losses in some seasons In the summer of 2014 the sexual stage of this fungus was observed for the first time in New Zealand Subsequent surveys showed the sexual state as widespread in Gisborne Hawkes Bay and Marlborough...

Bryoclaviculus campylopi, a tiny, beautiful inoperculate discomycete fungus found only in association with the moss Campylopus acuminatus, is described as a new genus and species from New Zealand. Phylogenetically it has a sister relationship with the northern hemisphere moss-associated species Bryoglossum gracile. It is distinguished macroscopical...

Phylogenetic analysis shows that Lanzia berggrenii is closely related to the core Hymenoscyphus clade, rather than the Rutstroemiceae, despite this species being associated with the development of stromatic tissue on its host substrate. Accepted here in the genus Hymenoscyphus, H. berggrenii and four newly described species from New Zealand form a...

A species concept for Phytophthora "taxon Agathis" – causal agent of kauri dieback in New Zealand 1 • Phytophthora "taxon Agathis" (PTA) has been identifi ed (Beever et al. 2009) as a causal agent of kauri (Agathis australis) dieback in northern New Zealand (Figs 1 & 2). • Originally misidentifi ed as the morphologically similar P. heveae (Gadgil 1...

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 l...

The development of protocols for the conservation of fungi requires knowledge of the factors controlling their distribution, diversity, and community composition. Here we compare patterns of variation in fungal communities across New Zealand's Nothofagus forests, reportedly the most myco-diverse in New Zealand and hence potentially key to effective...

Hypoderma siculum is described and illustrated as a new species from southeast Sicily (Italy) that occurs on remnants of Ferula communis (Apiaceae). Its ecology and taxonomic and phylogenetic relationships are discussed

Two new pathogens, Guignardia korthalsellae and Rosenscheldiella korthalsellae, are described from New Zealand's pygmy mistletoes (Korthalsella, Viscaceae). Both form ascomata on living phylloclades with minimal disruption of the tissue. Fungal hyphae within the phylloclade are primarily intercellular. Guignardia korthalsellae disrupts a limited nu...

Subsequent to the detection of Pseudomonas syringae pv. actinidiae (Psa) on kiwifruit in Te Puke (November 2010), isolates of Pseudomonas spp. from kiwifruit stored in the International Collection of Microorganisms from Plants (ICMP) and at Plant & Food Research (PFR) were tested by PCR for Psa. A total of 139 isolates from ICMP were assayed with t...

Symptoms resembling papaya bacterial crown rot (1,3) attributed to Erwinia papayae were first observed on ‘Waimanalo’ and ‘Solo Sunrise’ papaya on the island of Tongatapu, Kingdom of Tonga in July 2009. Spreading, dark green, water-soaked lesions formed on juvenile stem tissue and developed into a foul-smelling, wet rot that destroyed large section...

Kauri dieback is an increasing problem affecting kauri (Agathis australis) in Auckland and Northland (Fig. 1). Phytophthora taxon Agathis (PTA) has been identified (by Ross Beever) as a causal agent of kauri dieback, but we do not know if PTA is a new endemic species or whether it has been described elsewhere and was introduced to New Zealand.

A new genus, Claviradulomyces, morphologically typical of Odontotremataceae, is proposed to accommodate the new species Claviradulomyces dabeicola. The genus is characterised by its ornamented periphysoids, and long-cylindric, sigmoid, acuminate ascospores. Genetically, C. dabeicola falls within the Ostropales, but the Odontotremataceae have been v...

Pyriculara cortaderiae sp. nov. found on leaves of Cortaderia selloana in New Zealand, is illustrated and described and compared with related taxa. rDNA sequencing showed it to be distinct from other species. It was associated with a narrow, dark brown leaf streak.

Surveys of fungi associated with stained vascular tissue in kiwifruit vines in New Zealand have consistently revealed Phialophora-like fungi. Phylogenetic analyses based on DNA sequences have shown most of these to be Leotiomycetes. The teleomorph of the most common species isolated from stained kiwifruit wood has been found on fallen wood in nativ...

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and i...

Strains of Xanthomonas isolated in New Zealand from diseased endemic and introduced plants, investigated in a multi-locus sequence analysis (MLSA), were distributed primarily in two species. Strains from Dysoxylum, Hardenbergia, Liquidambar, Magnolia and Mahonia were members of Xanthomonas arboricola. Strains of Xanthomonas campestris pv. laureliae...

Ecology Letters (2010) 13: 675–684 Community assembly history is increasingly recognized as a fundamental determinant of community structure. However, little is known as to how assembly history may affect ecosystem functioning via its effect on community structure. Using wood-decaying fungi as a model system, we provide experimental evidence that l...

A real problem with understanding the distribution of fungal species is a lack of specimens and associated collecting data. Few people can accurately identify fungi, and the effort required to collect and store a specimen is high, meaning even the most common species are poorly represented in New Zealand's fungal collections. This, in turn, creates...

The diversity and distribution of fungal endophytes in the leaves of four podocarps (Dacrydium cupressinum, Prumnopitys ferruginea, Dacrycarpus dacrydioides, and Podocarpus totara, all Podocarpaceae) and an angiosperm (Kunzea ericoides, Myrtaceae) occurring in close stands were studied. The effects of host species, locality, and season on endophyte...

Name: IMI393994_LSU.

A multilocus sequence analysis (MLSA) of strains representing all validly published Xanthomonas spp. (119 strains) was conducted using four genes; dnaK, fyuA, gyrB and rpoD, a total of 440 sequences. Xanthomonas spp. were divided into two groups similar to those indicated in earlier 16S rDNA comparative analyses, and they possibly represent distinc...

The New Zealand stick insect genus Acanthoxyla Uvarov is extremely unusual among higher taxa of animals in that all known species are obligate parthenogens. We have used a combination of the mitochondrial DNA genes cytochrome oxidase subunits I and II, 28S nuclear ribosomal RNA, and the two single-copy nuclear genes elongation factor 1alpha and pho...