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Stone cells are the brachysclereid cells in pear (Pyrus) fruit, consisting almost entirely of lignified secondary cell walls. They are distributed mainly near the fruit core and spread radially in the whole fruit. However, the development of stone cells has not been comprehensively characterized, and little is known about the regulation of stone cell formation at the transcriptomic, proteomic, and metabolomic levels. In the present study, we performed phenomic analysis on the stone cells and their associated vascular bundles distributed near the fruit cores. Transcriptomic, proteomic, and metabolomic analyses revealed a significant positive regulation of biological processes which contribute to the lignification and lignin deposition in stone cells near the fruit core, including sucrose metabolism and phenylalanine, tyrosine, tryptophan, and phenylalanine biosynthesis. We found many metabolites generated from the phenylpropanoid pathway contributing to the cell wall formation of stone cells near the fruit core. Furthermore, we identified a key transcription factor, PbbZIP48, which was highly expressed near the fruit core and was shown to regulate lignin biosynthesis in stone cells. In conclusion, the present study provides insight into the mechanism of lignified stone cell formation near the pear fruit core at multiple levels., (© 2022 Society for Experimental Biology and John Wiley & Sons Ltd.)

Plant-parasitic nematodes have been causing more economic losses and related damages to fruit crops in the Province of Ontario than previous estimates. We have been conducting surveys since 2019 for the presence of plant-parasitic nematodes in different orchards in the Niagara region. Collected soil samples were extracted for nematodes following Jenkins (1964). Among the plant-parasitic nematodes identified, we detected ring nematodes (Mesocriconema species) in 87% of the soil samples collected from different apricots fields, ranging from 20 to 200 ring nematode per kg of soil. The apricot cultivar was Haroblush and did not show any symptoms of nematode infestation. The morphometric measurements (mean in μm ± standard deviation, range) of the ring nematodes (adult females), n = 27), body length = (605 +/- 23, 550 - 650), stylet = (75 +/- 8, 65 - 79), a (total body length divided by maximum body diameter = 12 +/- 1.5, 10.2 - 13.9), b (total body length divided by pharyngeal length = 3.6 +/- 0.5, 3.2 - 3.9), c = 20, V (percentage of length from anterior end to vulva position in total body length) = 92 +/- 1.3,91 - 93), R (total body annules = 105 +/- 5, 100 - 110), Rvan (total annules between vulva and anus = 2), and Ran (total annules between anus and tail terminus = 5). Lips sclerotized, with conspicuous and elevated labial disc surrounding the oral aperture, sub-lateral lobes also conspicuous. The stylet was long and robust. Excretory pore was located between 30-31 annuli from the anterior end. The vulva located either between 6 and 7, but mostly between 7 and 8 annuli from the posterior end. The juveniles were similar to the females in body shape with: sub-lateral lobes present, stylet 55-60 µm long, total annuls 80-90, and fine longitudinal lines were observed. Based on the morphology (Figure 1) and morphometric characteristics, the nematode species was identified as Mesocriconema xenoplax, which was consistent with the description by Raski (1952). To further confirm, DNA was extracted from a total of 20 nematodes (females and juveniles), the D2-D3 expansion segment of 28S rDNA amplified using the primer pair: D2A: 5´-ACAAGTACCGTGAGGGAAAGT TG-3', D3B: 5'-TCCTCGGAAGGAACCAGCTACTA-3' (Nunn, 1992). The PCR product was purified and sequenced. The resulting sequence was deposited into the GenBank database and assigned with accession number ON130754. A BLAST search in the NCBI database revealed 99% similarity to sequences of M. xenoplax with accession numbers MH819082.1 and FN433854.1 from South Africa and California, respectively. Eight Haroblush plants were each inoculated with 100 ring nematodes/kg in 5-gallon pots. Haroblush without nematode were maintained as control. The nematode reproduction and symptoms were assessed after 6 and 24 months. The plants did not show below or aboveground symptoms after 6 months. However, root growth reduction, necrosis and death of feeder roots were observed after 24 months when compared to the control. Nematodes extracted from the soil had a mean of 512±48 and 1593±162 ring nematode/kg after 6 and 24 months, respectively, an indication of susceptibility. Mesocriconema xenoplax can cause 85% reduction in root biomass, and yield losses can occur at higher infestations (Pinkerton et al., 2004). Regardless, the potential impact and distribution of this nematode on apricots growth and yield in Ontario are not documented yet. To the best of our knowledge, this is the first report of the ring nematode M. xenoplax on apricots from Ontario, Canada.

Penicillium species were commonly isolated during a fungal survey of bat hibernacula in New Brunswick and Quebec, Canada. Strains were isolated from arthropods, bats, rodents ( i.e . the deer mouse Peromyscus maniculatus ), their dung, and cave walls. Hundreds of fungal strains were recovered, of which Penicillium represented a major component of the community. Penicillium strains were grouped by colony characters on Blakeslee's malt extract agar. DNA sequencing of the secondary identification marker, beta-tubulin, was done for representative strains from each group. In some cases, ITS and calmodulin were sequenced to confirm identifications. In total, 13 species were identified, while eight strains consistently resolved into a unique clade with P. discolor , P. echinulatum and P. solitum as its closest relatives. Penicillium speluncae is described using macroand micromorphological characters, multigene phylogenies (including ITS, beta-tubulin, calmodulin and RNA polymerase II second largest subunit) and extrolite profiles. Major extrolites produced by the new species include cyclopenins, viridicatins, chaetoglobosins, and a microheterogenous series of cyclic and linear tetrapeptides., (© 2020 Westerdijk Fungal Biodiversity Institute.)

Berkleasmium is a polyphyletic genus comprising 37 dematiaceous hyphomycetous species. In this study, independent collections of the type species, B. concinnum , were made from Eastern North America. Nuclear internal transcribed spacer rDNA (ITS) and partial nuc 28S large subunit rDNA (LSU) sequences obtained from collections and subsequent cultures showed that Berkleasmium concinnum is the asexual morph of Neoacanthostigma septoconstrictum ( Tubeufiaceae , Tubeufiales ). Phylogenies inferred from Bayesian inference and maximum likelihood analyses of ITS-LSU sequence data confirmed this asexual-sexual morph connection and a re-examination of fungarium reference specimens also revealed the co-occurrence of N. septoconstrictum ascomata and B. concinnum sporodochia. Neoacanthostigma septoconstrictum is therefore synonymized under B. concinnum on the basis of priority. A specimen identified as N. septoconstrictum from Thailand is described as N. thailandicum sp. nov., based on morphological and genetic distinctiveness.

Development and use of resistant wheat cultivars is the most practical and economical approach for the control of Fusarium head blight (FHB). In the present study, a population of recombinant inbred lines derived from the cross between 'AC Brio' (a Canadian bread wheat cultivar moderately susceptible to FHB) and 'TC 67' (an FHB-resistant cultivar derived from Triticum timopheevii) was used to map quantitative trait loci (QTL) for FHB resistance using microsatellite molecular markers. Multiple interval mapping detected several QTL for FHB resistance on the chromosomes 5AL and 6A. The QTL detected in the marker interval of cfd6.1-barc48 on chromosome 5AL explained 10.9, 5.2, and 7.8% of phenotypic variation for disease incidence (type I resistance), disease severity (a combination of type I and type II resistance), and Fusarium-damaged kernels (FDK) (type IV resistance) under field conditions, respectively. The second QTL mapped to 5AL, in the marker interval of cfd39-cfa2185, explained 19.4 and 20.6% of phenotypic variation for FDK under field conditions and disease severity in the greenhouse (type II resistance), respectively. The QTL located on chromosome 6A conferred resistance to disease incidence and severity under field conditions and to disease severity in the greenhouse, explaining 6.8 to 11.8% of phenotypic variation for these traits. Several QTL for agronomic traits were also mapped in this study, including one and two QTL to the chromosomes 2A and 5AL, respectively, all for plant height, and two QTL to chromosome 6A for plant height and flowering date, respectively. The 5AL QTL for FHB resistance mapped in the marker interval of cfd39-cfa2185 in the present study is a novel QTL that originated from T. timopheevii and is reported here for the first time. Further validation of this QTL is required for wheat breeding programs to enhance resistance levels to FHB.

Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most devastating diseases of wheat and barley. Resistance to FHB is highly complex and quantitative in nature, and is most often classified as resistance to spikelet infection and resistance to spread of pathogen through the rachis. In the present study, a resistant (CI9831) and a susceptible (H106-371) two-row barley genotypes, with contrasting levels of spikelet resistance to FHB, pathogen or mock-inoculated, were profiled for metabolites based on liquid chromatography and high resolution mass spectrometry. The key resistance-related (RR) metabolites belonging to fatty acids, phenylpropanoids, flavonoids and terpenoid biosynthetic pathways were identified. The free fatty acids (FFAs) linoleic and palmitic acids were among the highest fold change RR induced (RRI) metabolites. These FFAs are deposited as cutin monomers and oligomers to reinforce the cuticle, which acts as a barrier to pathogen entry. Quantitative real-time PCR studies revealed higher expressions of KAS2, CYP86A2, CYP89A2, LACS2 and WAX INDUCER1 (HvWIN1) transcription factor in the pathogen-inoculated resistant genotype than in the susceptible genotype. Knockdown of HvWIN1 by virus-induced genes silencing (VIGS) in resistant genotype upon pathogen inoculation increased the disease severity and fungal biomass, and decreased the abundance of FFAs like linoleic and palmitic acids. Notably, the expression of CYP86A2, CYP89A2 and LAC2 genes was also suppressed, proving the link of HvWIN1 in regulating these genes in cuticle biosynthesis as a defense response., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

The genus Torulomyces was characterised by species that typically have conidiophores consisting of solitary phialides that produce long chains of conidia connected by disjunctors. Based on the phylogenetic position of P. lagena (generic ex-neotype), the genus and its seven species were transferred to Penicillium and classified in sect. Torulomyces along with P. cryptum and P. lassenii. The aim of this study was to review the species currently classified in sect. Torulomyces using morphology and phylogenies of the ITS, BenA, CaM and RPB2 regions. Based on our results, we accept 16 species in sect. Torulomyces, including 12 new species described as P. aeris, P. austricola, P. cantabricum, P. catalonicum, P. oregonense, P. marthae-christenseniae, P. riverlandense, P. tubakianum, P. variratense, P. williamettense, P. wisconsinense and P. wollemiicola. In addition, we reclassify P. laeve and P. ovatum in sect. Exilicaulis and correct the typification of P. lagena. We provide descriptions and notes on the identification of the species.

The Arabidopsis pollen grain is covered by a lipidic pollen coat representing select constituents released upon the programmed cell death of the anther secretory tapetum. These constituents originate primarily from two specialized tapetal organelles, elaioplasts and tapetosomes. Tapetosomes are distinctive Brassicaceae organelles derived from the endoplasmic reticulum that store triacylglycerols, flavonoids, alkanes, and proteins. The tapetosome triacylglycerols are found within lipid droplets surrounded by the highly variable tapetal oleosins that eventually generate the most abundant proteins of the pollen coat. Many questions remain regarding the sub-cellular targeting of tapetal oleosins as well as their role in tapetosome formation. Translational fusions of different tapetal oleosins or their derived domains to marker proteins were introduced into Arabidopsis thaliana to investigate their localization, processing and function. Arabidopsis tapetal oleosins were shown to be proteolytically cleaved following tapetum degeneration and different protein domains were targeted to the pollen coat despite vast differences in composition and size. Importantly, specific fusions were discovered to affect distinct aspects of tapetosome formation. This report not only highlighted the critical role of individual tapetal oleosin domains in Arabidopsis tapetosome formation, but revealed translational fusions to be a valuable tool in deciphering this evidently complex developmental process., (© 2015 Government of Canada, Ministry of Agriculture and AgriFood Canada. New Phytologist © 2015 New Phytologist Trust.)

A list of 254 names of species and two names of varieties in Trichoderma with name or names against which they are to be protected, following the ICN (Melbourne Code, Art. 14.13), is presented for consideration by the General Committee established by the Congress, which then will refer them to the Nomenclature Committee for Fungi (NCF). This list includes 252 species, one variety and one form. Two new names are proposed: T. neocrassum Samuel (syn. Hypocrea crassa P. Chaverri & Samuels), T. patellotropicum Samuels (syn. Hypocrea patella f. tropica Yoshim. Doi). The following new combinations in Trichoderma are proposed: T. brevipes (Mont.) Samuels, T. cerebriforme (Berk.) Samuels, T. latizonatum (Peck) Samuels, and T. poronioideum (A. Möller) Samuels. The following species are lectotypified: T. americanum (Canham) Jaklitsch & Voglmayr, Gliocladium flavofuscum J.H. Miller, Giddens & A.A. Foster, T. inhamatum Veerkamp & W. Gams, T. konilangbra Samuels, O. Petrini & C.P. Kubicek, T. koningii Oudem., T. pezizoides (Berk. & Broome) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr and T. virens (J.H. Miller, Giddens & A.A. Foster) Arx. Epitypes are proposed for the following species: T. albocorneum (Yoshim. Doi) Jaklitsch & Voglmayr, T. albofulvum (Berk. & Broome) Jaklitsch & Voglmayr, T. atrogelatinosum (Dingley) Jaklitsch & Voglmayr, T. corneum (Pat.) Jaklitsch & Voglmayr, T. cornu-damae (Pat.) Z.X. Zhu & W.Y. Zhuang, T. flaviconidium (P. Chaverri, Druzhinina & Samuels) Jaklitsch & Voglmayr, T. hamatum (Bonord.) Bain., T. hunua (Dingley) Jaklitsch & Voglmayr, T. patella (Cooke & Peck) Jaklitsch & Voglmayr, Hypocrea patella f. tropica Yoshim. Doi, T. polysporum (Link) Rifai, T. poronioideum (A. Möller) Samuels T. semiorbis (Berk.) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr, and T. tropicosinense (P.G. Liu) P.G. Liu, Z.X. Zhu & W.Y. Zhuang.

Fusarium graminearum is a pathogenic fungus that causes Fusarium head blight in wheat and lowers the yield and quality of grains by contamination with the trichothecene mycotoxin deoxynivalenol. The fungi coexist and interact with several different fusaria as well as other plant pathogenic fungi and bacteria in the field. In Canada, F. graminearum exists as two main trichothecene chemotypes: 3-acetyldeoxynivalenol and 15-acetyldeoxynivalenol. To understand the potential interactions between two isolates of these chemotypes, we conducted coinoculation studies both in culture and in planta. The studies showed that intraspecies interaction reduces trichothecene yield in culture and disease symptoms in wheat. To elucidate the genes involved in the intraspecies interaction, expression profiling was performed on RNA samples isolated from coinoculated cultures, and potential genes were identified by using the genome sequences of the respective isolates.

Agriculture in rainfed dry areas is often challenged by inadequate water and nutrient supplies. Summerfallowing has been used to conserve rainwater and promote the release of nitrogen via the N mineralization of soil organic matter. However, summerfallowing leaves land without any crops planted for one entire growing season, creating lost production opportunity. Additionally, summerfallowing has serious environmental consequences. It is unknown whether alternative systems can be developed to retain the beneficial features of summerfallowing with little or no environmental impact. Here, we show that diversifying cropping systems with pulse crops can enhance soil water conservation, improve soil N availability, and increase system productivity. A 3-yr cropping sequence study, repeated for five cycles in Saskatchewan from 2005 to 2011, shows that both pulse- and summerfallow-based systems enhances soil N availability, but the pulse system employs biological fixation of atmospheric N2, whereas the summerfallow-system relies on 'mining' soil N with depleting soil organic matter. In a 3-yr cropping cycle, the pulse system increased total grain production by 35.5%, improved protein yield by 50.9%, and enhanced fertilizer-N use efficiency by 33.0% over the summerfallow system. Diversifying cropping systems with pulses can serve as an effective alternative to summerfallowing in rainfed dry areas.

Colletotrichum lentis is a fungal pathogen of lentil in Canada but rarely reported elsewhere. Two races, Ct0 and Ct1, have been identified using differential lines. Our objective was to develop a PCR-probe differentiating these races. Sequences of the translation elongation factor 1α (tef1α), RNA polymerase II subunit B2 (rpb2), ATP citrate lyase subunit A (acla), and internal transcribed spacer (ITS) regions were monomorphic, while the intergenic spacer (IGS) region showed length polymorphisms at two minisatellites of 23 and 39 nucleotides (nt). A PCR-probe (39F/R) amplifying the 39 nt minisatellite was developed which subsequently revealed 1-5 minisatellites with 1-12 repeats in C. lentis. The probe differentiated race Ct1 isolates having 7, 9 or 7+9 repeats from race Ct0 having primarily 2 or 4 repeats, occasionally 5, 6, or 8, but never 7 or 9 repeats. These isolates were collected between 1991 and 1999. In a 2012 survey isolates with 2 and 4 repeats increased from 34% to 67%, while isolated with 7 or 9 repeats decreased from 40 to 4%, likely because Ct1 resistant lentil varieties had been grown. The 39 nt repeat was identified in C. gloeosporioides, C. trifolii, Ascochyta lentis, Sclerotinia sclerotiorum and Botrytis cinerea. Thus, the 39F/R PCR probe is not species specific, but can differentiate isolates based on repeat number. The 23 nt minisatellite in C. lentis exists as three length variants with ten sequence variations differentiating race Ct0 having 14 or 19 repeats from race Ct1 having 17 repeats, except for one isolate. RNA-translation of 23 nt repeats forms hairpins and has the appropriate length to suggest that IGS could be a site of small RNA synthesis, a hypothesis that warrants further investigation. Small RNA from fungal plant pathogens able to silence genes either in the host or pathogen thereby aiding infection have been reported.

Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

Basidioascus undulatus is a soil basidiomycete belonging to the order Geminibasidiales. The taxonomic status of the order was unclear as originally it was only tentatively classified in the class Wallemiomycetes. The fungi in Geminibasidiales have an ambiguously defined sexual cycle. In this study, we sequenced the genome of B. undulatus to gain insights into its sexuality and evolutionary origins. The assembled genome draft was approximately 32 Mb in size, had a median nucleotide coverage of 24X, and contained 6123 predicted genes. Previous morphological descriptions of B. undulatus relied on interpretation of putative sexual structures. In this study, nuclear staining and confocal microscopy showed meiosis occurring in basidia and genome analysis confirmed the existence of genes involved in meiosis and mating. Using 35 protein-coding genes extracted from genomic information, phylogenomic and molecular dating analyses confirmed that B. undulatus indeed belongs to a lineage distantly related to Wallemia while retaining a basal position in Agaricomycotina. These results, combined with differences in septal pore morphology, led us to move the order Geminibasidiales out of the Wallemiomycetes and into the new class Geminibasidiomycetes cl. nov. Finally, the concept of Agaricomycotina is emended to include both Wallemiomycetes and Geminibasidiomycetes.

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 ridges. Ribosomal DNA sequences place the new species within Onygenales, but comparison with the known genetic diversity within the order linked it to no existing genus or family. It is the first species of Onygenales reported from the shells of terrestrial snails. This fungus has been listed as Critically Endangered in New Zealand and has been previously referred to as 'Trichocomaceae gen. nov.' in those threat lists.

Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor (MCM7), pre-rRNA processing protein (TSR1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.

Soft X-ray absorption spectroscopy coupled with nano-scale microscopy has been widely used in material science, environmental science, and physical sciences. In this work, the advantages of soft X-ray absorption spectromicroscopy for plant biopolymer research were demonstrated by determining the chemical sensitivity of the technique to identify common plant biopolymers and to map the distributions of biopolymers in plant samples. The chemical sensitivity of soft X-ray spectroscopy to study biopolymers was determined by recording the spectra of common plant biopolymers using soft X-ray and Fourier Transform mid Infrared (FT-IR) spectroscopy techniques. The soft X-ray spectra of lignin, cellulose, and polygalacturonic acid have distinct spectral features. However, there were no distinct differences between cellulose and hemicellulose spectra. Mid infrared spectra of all biopolymers were unique and there were differences between the spectra of water soluble and insoluble xylans. The advantage of nano-scale spatial resolution exploited using soft X-ray spectromicroscopy for plant biopolymer research was demonstrated by mapping plant cell wall biopolymers in a lentil stem section and compared with the FT-IR spectromicroscopy data from the same sample. The soft X-ray spectromicroscopy enables mapping of biopolymers at the sub-cellular (~30 nm) resolution whereas, the limited spatial resolution in the micron scale range in the FT-IR spectromicroscopy made it difficult to identify the localized distribution of biopolymers. The advantages and limitations of soft X-ray and FT-IR spectromicroscopy techniques for biopolymer research are also discussed.

A worldwide survey of Wallemia occurring in house dust and indoor air was conducted. The isolated strains were identified as W. sebi and W. muriae. Previous studies suggested that the W. sebi phylogenetic clade contained cryptic species but conclusive evidence was lacking because only the internal transcribed spacer (ITS) marker was analyzed. The ITS and four protein-coding genes (MCM7, RPB1, RPB2, and TSR1) were sequenced for 85 isolates. Based on an initial neighbor joining analysis of the concatenated genes, W. muriae remained monophyletic but four clades were found in W. sebi, which we designated as W. sebi clades 1, 2, 3, and 4. We hypothesized that these clades represent distinct phylogenetic species within the Wallemia sebi species complex (WSSC). We then conducted multiple phylogenetic analyses and demonstrated genealogical concordance, which supports the existence of four phylogenetic species within the WSSC. Geographically, W. muriae was only found in Europe, W. sebi clade 3 was only found in Canada, W. sebi clade 4 was found in subtropical regions, while W. sebi clade 1 and 2 were found worldwide. Haplotype analysis showed that W. sebi clades 1 and 2 had multiple haplotypes while W. sebi clades 3 and 4 had one haplotype and may have been under sampled. We describe W. sebi clades 2, 3, and 4 as new species in a companion study.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Three Nomenclature Sessions were convened during the 10(th) International Mycological Congress (IMC10) in Bangkok on 3-8 August 2014. In addition a Questionnaire was given to all delegates. This Report reviews and summarizes the views expressed in the Sessions and in the responses to the Questionnaire. The issues covered related to aspects of: registration, protected names, forgotten names, pleomorphic fungi, lichenized fungi, typification, diagnoses, and governance. In addition, reports were received from working groups preparing lists of names to be proposed for protection, and controversial cases of competing names were discussed. The Congress was mandated to ratify decisions of the Nomenclature Committee for Fungi (NCF) on the appointment of repositories for the registration of new fungal names. After discussion in the Sessions on the decision of the NCF to appoint three such bodies, a Resolution to that effect was approved by the Congress. The Congress also adopted a Resolution asking that the opinions of mycologists on future directions for the nomenclature of fungi be taken into account in formulating changes in the rules for consideration at the International Botanical Congress in 2017.

Two mutants (tri6Δ and noxABΔ) of the fungal pathogen Fusarium graminearum were assessed for their ability to prime immune responses in wheat (cv. Roblin) against challenge with pathogenic F. graminearum. Priming treatments generated Fusarium head blight (FHB)-resistant wheat phenotypes and reduced the accumulation of fungal mycotoxins in infected tissues. Microarray analysis identified 260 transcripts that were differentially expressed during the priming period. Expression changes were observed in genes associated with immune surveillance systems, signalling cascades, antimicrobial compound production, oxidative burst, secondary metabolism, and detoxification and transport. Specifically, genes related to jasmonate, gibberellin and ethylene biosynthesis exhibited differential expression during priming. In addition, the induction of the phenylpropanoid pathways that lead to flavonoid, coumarin and hydroxycinnamic acid amide accumulation was also observed. This study highlights the utility of nonpathogenic mutants to both elicit and delineate stages of defence responses in wheat., (© 2014 HER MAJESTY THE QUEEN IN RIGHT OF CANADA MOLECULAR PLANT PATHOLOGY © 2014 BSPP AND JOHN WILEY & SONS LTD.)

Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

Wheat is one of the world's most favoured food sources, reaching millions of people on a daily basis. However, its production has climatic consequences. Fuel, inorganic fertilizers and pesticides used in wheat production emit greenhouse gases that can contribute negatively to climate change. It is unknown whether adopting alternative farming practices will increase crop yield while reducing carbon emissions. Here we quantify the carbon footprint of alternative wheat production systems suited to semiarid environments. We find that integrating improved farming practices (that is, fertilizing crops based on soil tests, reducing summerfallow frequencies and rotating cereals with grain legumes) lowers wheat carbon footprint effectively, averaging -256 kg CO2 eq ha(-1) per year. For each kg of wheat grain produced, a net 0.027-0.377 kg CO2 eq is sequestered into the soil. With the suite of improved farming practices, wheat takes up more CO2 from the atmosphere than is actually emitted during its production.

Soybean isolines with different combinations of photoperiod sensitivity alleles were planted in a greenhouse at different times during the year resulting in natural variation in daily incident irradiance and duration. The time from planting to first flower were observed. Mathematical models, using additive and multiplicative modes, were developed to quantify the effect of photoperiod, temperature, photoperiod-temperature interactions, rate of photoperiod change, and daily solar irradiance on flowering time. Observed flowering times correlated with predicted times (R² = 0.92, Standard Error of the Estimate (SSE) = 2.84 d, multiplicative mode; R² = 0.91, SSE = 2.88 d, additive mode). The addition of a rate of photoperiod change function and an irradiance function to the temperature and photoperiod functions improved the accuracy of flowering time prediction. The addition of a modified photoperiod function, which allowed for photoperiod sensitivity at shorter photoperiods, improved prediction of flowering time. Both increasing and decreasing rate of photoperiod change, as well as low levels of daily irradiance delayed flowering in soybean. The complete model, which included terms for the rate of photoperiod change, photoperiod, temperature and irradiance, predicted time to first flower in soybean across a range of environmental conditions with an SEE of 3.6 days when tested with independent data.

To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

We examined three different-ploidy wheat species to elucidate the development of aboveground architecture and its domesticated mechanism under environment-controlled field conditions. Architecture parameters including leaf, stem, spike and canopy morphology were measured together with biomass allocation, leaf net photosynthetic rate and instantaneous water use efficiency (WUE(i)). Canopy biomass density was decreased from diploid to tetraploid wheat, but increased to maximum in hexaploid wheat. Population yield in hexaploid wheat was higher than in diploid wheat, but the population fitness and individual competition ability was higher in diploid wheats. Plant architecture was modified from a compact type in diploid wheats to an incompact type in tetraploid wheats, and then to a more compact type of hexaploid wheats. Biomass accumulation, population yield, harvest index and the seed to leaf ratio increased from diploid to tetraploid and hexaploid, associated with heavier specific internode weight and greater canopy biomass density in hexaploid and tetraploid than in diploid wheat. Leaf photosynthetic rate and WUEi were decreased from diploid to tetraploid and increased from tetraploid to hexaploid due to more compact leaf type in hexaploid and diploid than in tetraploid. Grain yield formation and WUEi were closely associated with spatial stance of leaves and stems. We conclude that the ideotype of dryland wheats could be based on spatial reconstruction of leaf type and further exertion of leaf photosynthetic rate.

Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.

Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Aspergillus comprises a diverse group of species based on morphological, physiological and phylogenetic characters, which significantly impact biotechnology, food production, indoor environments and human health. Aspergillus was traditionally associated with nine teleomorph genera, but phylogenetic data suggest that together with genera such as Polypaecilum, Phialosimplex, Dichotomomyces and Cristaspora, Aspergillus forms a monophyletic clade closely related to Penicillium. Changes in the International Code of Nomenclature for algae, fungi and plants resulted in the move to one name per species, meaning that a decision had to be made whether to keep Aspergillus as one big genus or to split it into several smaller genera. The International Commission of Penicillium and Aspergillus decided to keep Aspergillus instead of using smaller genera. In this paper, we present the arguments for this decision. We introduce new combinations for accepted species presently lacking an Aspergillus name and provide an updated accepted species list for the genus, now containing 339 species. To add to the scientific value of the list, we include information about living ex-type culture collection numbers and GenBank accession numbers for available representative ITS, calmodulin, β-tubulin and RPB2 sequences. In addition, we recommend a standard working technique for Aspergillus and propose calmodulin as a secondary identification marker.

Leafhoppers (Hemiptera: Cicadellidae) are pests of many temperate crops, including grapevines (Vitis species). Uncontrolled populations can induce direct and indirect damage to crops due to feeding that results in significant yield losses and increased mortality in infected vineyards due to virus, bacteria, or phytoplasmas vectored by leafhoppers. The main objective of this work was to determine the diversity of leafhoppers found in vineyards of the three main Canadian production provinces, i.e., in British Columbia, Ontario, and Quebec. Approximately 18,000 specimens were collected in 80 commercial vineyards from 2006 to 2008. We identified 54 genera and at least 110 different species associated with vineyards, among which 22 were predominant and represented more than 91% of all the leafhoppers. Species richness and diversity were estimated by both Shannon's and Pielou's indices. For each province, results indicated a temporal variation in species composition. Color photographs provide a tool to quickly identify 72 leafhoppers commonly associated with vineyards., (This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.)

The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals., (Copyright © 2014 Adam et al.)

We propose that targeting the enhanced photosynthetic performance associated with the cold acclimation of winter cultivars of rye (Secale cereale L.), wheat (Triticum aestivum L.), and Brassica napus L. may provide a novel approach to improve crop productivity under abiotic as well as biotic stress conditions. In support of this hypothesis, we provide the physiological, biochemical, and molecular evidence that the dwarf phenotype induced by cold acclimation is coupled to significant enhancement in photosynthetic performance, resistance to photoinhibition, and a decreased dependence on photoprotection through non-photochemical quenching which result in enhanced biomass production and ultimately increased seed yield. These system-wide changes at the levels of phenotype, physiology, and biochemistry appear to be governed by the family of C-repeat/dehydration-responsive family of transcription factors (CBF/DREB1). We relate this phenomenon to the semi-dwarf, gibberellic acid insensitive (GAI), cereal varieties developed during the "green revolution" of the early 1960s and 1970s. We suggest that genetic manipulation of the family of C-repeat/dehydration-responsive element binding transcription factors (CBF/DREB1) may provide a novel approach for the maintenance and perhaps even the enhancement of plant productivity under conditions of sub-optimal growth conditions predicted for our future climate.

Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.

A robust phenotypic plasticity to ward off adverse environmental conditions determines performance and productivity in crop plants. Flax (linseed), is an important cash crop produced for natural textile fiber (linen) or oilseed with many health promoting products. This crop is prone to drought stress and yield losses in many parts of the world. Despite recent advances in drought research in a number of important crops, related progress in flax is very limited. Since, response of this plant to drought stress has not been addressed at the molecular level; we conducted microarray analysis to capture transcriptome associated with induced drought in flax. This study identified 183 differentially expressed genes (DEGs) associated with diverse cellular, biophysical and metabolic programs in flax. The analysis also revealed especially the altered regulation of cellular and metabolic pathways governing photosynthesis. Additionally, comparative transcriptome analysis identified a plethora of genes that displayed differential regulation both spatially and temporally. These results revealed co-regulated expression of 26 genes in both shoot and root tissues with implications for drought stress response. Furthermore, the data also showed that more genes are upregulated in roots compared to shoots, suggesting that roots may play important and additional roles in response to drought in flax. With prolonged drought treatment, the number of DEGs increased in both tissue types. Differential expression of selected genes was confirmed by qRT-PCR, thus supporting the suggested functional association of these intrinsic genes in maintaining growth and homeostasis in response to imminent drought stress in flax. Together the present study has developed foundational and new transcriptome data sets for drought stress in flax.

In eastern Canada, soybean, Glycine max (L.) Merr., is the most important legume, and its cultivation is expanding to new regions as cultivars for the short growing season are developed. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is among the most destructive pests of soybean in the world. This nematode is also under quarantine regulations in many countries, including Canada. Until now, in Canada, SCN was only reported in the province of Ontario. Since its first detection in 1988 in the southwestern part of the province (1), SCN has been found in 12 other counties. It appears that SCN has been spreading in a north and northeast direction along the St. Lawrence River. We report here the first detection of SCN in the province of Quebec. Second stage juveniles (J2) and cysts were found in St. Anicet, Quebec, Canada, in a 10-ha soybean field. Light textured soil is a characteristic of the field, the same site where Pratylenchus alleni was recently discovered (2) and where irregular patches of stunted soybean plants were observed. Morphological and molecular studies of J2 and cysts confirmed the identification of this nematode population as SCN. The J2 were typical for SCN with a body length of 393 to 428 μm, lateral fields harboring four straight lines, a well-developed stylet 23 to 25 μm long, sub-ventral base knobs with posterior slops, a tail length of 43 to 50 μm, and a hyaline part of 23 to 29 μm. Cysts were brown and lemon-shaped with a posterior protuberance, ambifenestrated, underbridged, and had a strongly developed bullae. Key morphometrics were: a cyst fenestra 40 to 57 μm long and 28 to 44 μm wide, and a vulval slit 39 to 53 μm long. All of these are coincident with those of SCN (3). Ribosomal DNA of the ITS, 18S, and D2/D3 regions, and mitochondrial COX1 gene were PCR amplified from cysts and J2s gDNA using primers ITS-F (5'-TTGATTACGTCCCTGCCCTTT-3') and ITS-R (5'-ACGAGCCGAGTGATCCACCG-3'); 18S-F (5'-TTGGATAACTGTGGTTTAACTAG-3') and 18S-R (5'-ATTTCACCTCTCACGCAACA-3'); D2A (5'-ACAAGTACCGTGAGGGAAAGT-3') and D3B (5'-GACCCGTCTTGAAACACGGA-3'); and COXI-F (5'-CCTACTATGATTGGTGGTTTTGGTAATTG-3') and COX1-R (5'-GTAGCAGCAGTAAAATAAGCACG-3'), respectively, and sequenced. The nucleotide sequences were 98 to 100% similar to those of SCN found in NCBI nr database (July 2013). All the sequences have been submitted to GenBank with the following accession numbers: ITS (KF453621); 18S (KF453622); D2/D3 (KF453623); and COX1 (KF453624). Using species specific sequence characterized amplified region (SCAR) primers (4) also confirmed this was H. glycines. This is the first reported case of SCN in Quebec, Canada. The proximity of St. Anicet to the Ontario border is in accordance with the North/Northeastern dispersal hypothesis. The HG type of the SCN population will have to be determined before any resistant cultivars are deployed for the management of this pathogen in the province. References: (1) T. R. Anderson et al. Plant Dis. 72:453, 1988. (2) G. Bélair et al. Plant Dis. 97:292, 2013. (3) R. H. Mulvey. Can. J. Zool. 50:1277, 1972. (4) S. Ou et al. Nematology 10:397, 2008.

The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcasses, is reported here. The draft genome consists of 2.2 Mbp, with a 27.12% G+C content. A total of 2,179 protein-coding genes, 46 tRNA genes, and 15 rRNAs have been identified and annotated.

Arabidopsis thaliana GOLDEN2-LIKE (GLK1 and 2) transcription factors regulate chloroplast development in a redundant manner. Overexpression of AtGLK1 (35S:AtGLK1) in Arabidopsis also confers resistance to the cereal pathogen Fusarium graminearum. To further elucidate the role of GLK transcription factors in plant defence, the Arabidopsis glk1 glk2 double-mutant and 35S:AtGLK1 plants were challenged with the virulent oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) Noco2. Compared with Col-0, glk1 glk2 plants were highly resistant to Hpa Noco2, whereas 35S:AtGLK1 plants showed enhanced susceptibility to this pathogen. Genetic studies suggested that AtGLK-mediated plant defence to Hpa Noco2 was partially dependent on salicylic acid (SA) accumulation, but independent of the SA signalling protein NONEXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1). Pretreatment with jasmonic acid (JA) dramatically reversed Hpa Noco2 resistance in the glk1 glk2 double mutant, but only marginally affected the 35S:AtGLK1 plants. In addition, overexpression of AtGLK1 in the JA signalling mutant coi1-16 did not increase susceptibility to Hpa Noco2. Together, our GLK gain-of-function and loss-of-function experiments suggest that GLK acts upstream of JA signalling in disease susceptibility to Hpa Noco2. In contrast, glk1 glk2 plants were more susceptible to the necrotrophic fungal pathogen Botrytis cinerea, whereas 35S:AtGLK1 plants exhibited heightened resistance which could be maintained in the absence of JA signalling. Together, the data reveal that AtGLK1 is involved in JA-dependent susceptibility to the biotrophic pathogen Hpa Noco2 and in JA-independent resistance to the necrotrophic pathogen B. cinerea., (© 2013 HER MAJESTY THE QUEEN IN RIGHT OF CANADA. MOLECULAR PLANT PATHOLOGY © 2013 BSPP. REPRODUCED WITH THE PERMISSION OF THE MINISTER OF AGRICULTURE AND AGRI-FOOD CANADA.)

Unbiased lipidomic approaches have identified impairments in glycerophosphocholine second messenger metabolism in patients with Alzheimer's disease. Specifically, we have shown that amyloid-β42 signals the intraneuronal accumulation of PC(O-16:0/2:0) which is associated with neurotoxicity. Similar to neuronal cells, intracellular accumulation of PC(O-16:0/2:0) is also toxic to Saccharomyces cerevisiae, making yeast an excellent model to decipher the pathological effects of this lipid. We previously reported that phospholipase D, a phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2)-binding protein, was relocalized in response to PC(O-16:0/2:0), suggesting that this neurotoxic lipid may remodel lipid signaling networks. Here we show that PC(O-16:0/2:0) regulates the distribution of the PtdIns(4)P 5-kinase Mss4 and its product PtdIns(4,5)P2 leading to the formation of invaginations at the plasma membrane (PM). We further demonstrate that the effects of PC(O-16:0/2:0) on the distribution of PM PtdIns(4,5)P2 pools are in part mediated by changes in the biosynthesis of long chain bases (LCBs) and ceramides. A combination of genetic, biochemical and cell imaging approaches revealed that PC(O-16:0/2:0) is also a potent inhibitor of signaling through the Target of rampamycin complex 2 (TORC2). Together, these data provide mechanistic insight into how specific disruptions in phosphocholine second messenger metabolism associated with Alzheimer's disease may trigger larger network-wide disruptions in ceramide and phosphoinositide second messenger biosynthesis and signaling which have been previously implicated in disease progression.

Current literature accepts 17 species in Penicillium section Sclerotiora. Several produce colonies in bright yellow to orange colours and have monoverticillate conidiophores, apart from P. herquei, P. malachiteum and P. nodositatum, which are biverticillate. The focus of this paper is to refine the concepts of the species currently accepted in the section and introduce five new species, named after the Dutch Royal family as P. vanoranjei, P. maximae, P. amaliae, P. alexiae and P. arianeae. Penicillium vanoranjei produces orange (Dutch = oranje) colonies in culture, and is named after Willem-Alexander Claus George Ferdinand, 'Zijne Koninklijke Hoogheid de Prins van Oranje' (translated from Dutch as: 'His Royal Highness the Prince of Orange') and his family, to coincide with his coronation. We review the current taxonomic positions of P. lilacinoechinulatum and P. nodositatum, both currently considered to be synonyms of P. bilaiae. Sequence data generated in this study show that both species are phylogenetically distinct. Penicillium lilacinoechinulatum is closely related to P. amaliae sp. nov., whereas P. nodositatum does not belong to Penicillium sensu stricto. All species were compared morphologically and phylogenetically, based on β-tubulin and calmodulin DNA data. A table summarising the morphological characters of all species is included, together with photomicrographs and recommended DNA markers for identification.

Controlled tile drainage can boost crop yields and improve water quality, but it also has the potential to increase GHG emissions. This study compared in-situ chamber-based measures of soil CH4, N2O, and CO2 fluxes for silt loam soil under corn and soybean cropping with conventional tile drainage (UTD) and controlled tile drainage (CTD). A semi-empirical model (NEMIS-NOE) was also used to predict soil N2O fluxes from soils using observed soil data. Observed N2O and CH4 fluxes between UTD and CTD fields during the farming season were not significantly different at 0.05 level. Soils were primarily a sink for CH4 but in some cases a source (sources were associated exclusively with CTD). The average N2O fluxes measured ranged between 0.003 and 0.028 kg N ha(-1) day(-1). There were some significantly higher (p ≤ 0.05) CO2 fluxes associated with CTD relative to UTD during some years of study. Correlation analyses indicated that the shallower the water table, the greater the CO2 fluxes. Higher corn plant C for CTD tended to offset estimated higher CTD CO2 C losses via soil respiration by ∼100-300 kg C ha(-1). There were good fits between observed and predicted (NEMIS-NOE) N2O fluxes for corn (R(2) = 0.70) and soybean (R(2) = 0.53). Predicted N2O fluxes were higher for CTD for approximately 70% of the paired-field study periods suggesting that soil physical factors, such as water-filled pore space, imposed by CTD have potentially strong impacts on net N fluxes. Model predictions of daily cumulative N2O fluxes for the agronomically-active study period for corn-CTD and corn-UTD, as a percentage of total N fertilizer applied, were 3.1% and 2.6%, respectively. For predicted N2O fluxes on basis of yield units, indices were 0.0005 and 0.0004 (kg N kg(-1) crop grain yield) for CTD and UTD corn fields, respectively, and 0.0011 and 0.0005 for CTD and UTD soybean fields, respectively., (Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.)

The classification of brown leaf rust fungi (Puccinia recondita complex and allied species) on wheat (Triticum aestivum), rye (Secale cereale), and other grasses in the family Poaceae has experienced a long history of controversy and uncertainty due to the reduced morphological characteristics available for taxonomy and difficulty of conducting interfertility experiments. However, because these are pathogens on important crops, it is important to clarify the species delimitations reflecting the natural lineages. In this study, phylogenetic analyses were conducted with DNA sequence data from the ribosomal DNA internal transcribed spacer region and elongation factor 1-α to elucidate this species complex. Three phylogenetic lineages were recovered within the complex of rye leaf rust fungi, P. recondita sensu stricto, which is congruent with existing classifications based on DNA content, sexual compatibility, and morphological studies. The brown leaf rust fungus on wheat (P. triticina) grouped with the related species P. persistens on Elymus repens and E. intermedia as a strongly supported clade. Collections on other Elymus spp. were separated into six clades. Based on the phylogenetic affinities of nine type specimens and aecial host associations, potential taxonomic names were evaluated for selected lineages.

The genus Plutella was thought to be represented in Australia by a single introduced species, Plutella xylostella (Linnaeus), the diamondback moth. Its status as a major pest of cruciferous crops, and the difficulty in developing control strategies has motivated broad-ranging studies on its biology. Prior genetic work has generally supported the conclusion that populations of this migratory species are connected by substantial gene flow. However, the present study reveals the presence of two genetically divergent lineages of this taxonin Australia. One shows close genetic and morphological similarity with the nearly cosmopolitan Plutella xylostella. The second lineage possesses a similar external morphology, but marked sequence divergence in the barcode region of the cytochrome c oxidase I gene, coupled with clear differences in genitalia. As a consequence, members of this lineage are described as a new species, Plutella australiana Landry & Hebert, which is broadly distributed in the eastern half of Australia.

Despite their importance, there remains a paucity of large-scale gene expression-based studies of reproductive development in species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip(®) wheat genome array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages, and co-expressed as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. This comprehensive resource rests upon detailed gene annotations, and the expression profiles are readily accessible via a web browser., (© 2013 Her Majesty the Queen in Right of Canada as represented by the Minister of Agriculture and Agri-Food Canada.)

We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The "long" unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the "short" unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.