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.
View Article and Find Full Text PDFThere 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 complex, which causes the lung disease tuberculosis (TB) as well as non-tuberculous Mycobacteria (NTM) a growing cause of lung, skin, soft tissue, and other infections. Here we describe a medium-throughput bioluminescence-based pipeline to screen fungi for activity against Mycobacteria using the NTM species and We used this pipeline to screen 36 diverse fungal isolates from the International Collection of Microorganisms from Plants (ICMP) grown on a wide variety of nutrient-rich and nutrient-poor media and discovered that almost all the tested isolates produced considerable anti-mycobacterial activity.
View Article and Find Full Text PDFA second genus in Chlorociboriaceae is described here as 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 Chile ( , ) and one each from New Zealand ( ) and Australia ( ). They differ from species referred to , the only other genus in Chlorociboriaceae, in their terrestrial habitat and ascomata that are noticeably more hairy than the known species, most of which have apothecia with short, macroscopically indistinct hair-like elements.
View Article and Find Full Text PDFFungi in the class 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 character-poor samples increasingly relies on DNA sequencing.
View Article and Find Full Text PDFHigh-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 gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected.
View Article and Find Full Text PDFAnimal 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 underlying speciation. RNA-seq was used to generate the first male reproductive transcriptome for the New Zealand tree weta species Hemideina thoracica and H.
View Article and Find Full Text PDFThe 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 Burkholderia species complex, whi.
View Article and Find Full Text PDFCircoviruses 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 circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp.
View Article and Find Full Text PDFBackground: 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 a 700 meter elevational gradient.
Results: From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker.
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.
View Article and Find Full Text PDFHere, we report the draft genome sequence of Burkholderia andropogonis ICMP2807, a phytopathogenic bacterium isolated from Sorghum bicolor plants in the United States.
View Article and Find Full Text PDFHigh quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.
View Article and Find Full Text PDFComp Biochem Physiol Part D Genomics Proteomics
March 2013
The endemic New Zealand alpine stick insect Micrarchus nov. sp. 2 regularly experiences sub-zero temperatures in the wild.
View Article and Find Full Text PDFThe 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 conservation of fungi in New Zealand. Diversity of leaf endophytic fungi, as assessed by culturing on agar plates, is assessed for three Nothofagus sp.
View Article and Find Full Text PDFA 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.
View Article and Find Full Text PDFCommunity 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 large differences in ecosystem functioning can be caused by small differences in species immigration history during community assembly.
View Article and Find Full Text PDFThe 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 assemblages were investigated. Host species was the major factor shaping endophyte assemblages.
View Article and Find Full Text PDFThe 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 phosphoglucose isomerase to test hypotheses on the role of hybridization in the evolution of this genus. Alleles at the single-copy nuclear loci in three sampled species of Acanthoxyla were resolved by cloning the PCR products.
View Article and Find Full Text PDFA comprehensive collection of different methods for extracting high-quality genomic DNA from gram-positive and -negative bacteria and fungal mycelium and spores is described in this chapter. Special care has been taken in describing the ideal ratio of biological material to chemical reagents for an efficient extraction of genomic DNA, and in stating the appropriate application in molecular biology protocols (e.g.
View Article and Find Full Text PDFThe 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.
View Article and Find Full Text PDFFEMS Microbiol Lett
September 2004
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.
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