Improving ITS sequence data for identification of plant pathogenic fungi

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://unite.ut.ee),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.

Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae.The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are:Acantholichen,Ampulloclitocybe,Arrhenia,Cantharellula,Cantharocybe,Chromosera,Chrysomphalina,Cora,Corella,Cuphophyllus,Cyphellostereum,Dictyonema,Eonema,Gliophorus,Haasiella,Humidicutis,Hygroaster,Hygrocybe,Hygrophorus,Lichenomphalia,Neohygrocybe,Porpolomopsis and Pseudoarmillariella.A new genus that is sister to Chromosera is described as Gloioxanthomyces.Revisions were made at the ranks of subfamily,tribe,genus,subgenus,section and subsection.We present three new subfamilies,eight tribes(five new),eight subgenera(one new,one new combination and one stat.nov.),26 sections(five new and three new combinations and two stat.nov.)and 14 subsections(two new,two stat.nov.).Species of Chromosera,Gliophorus,Humidicutis,and Neohygrocybe are often treated within the genus Hygrocybe;we therefore provide valid names in both classification systems.We used a minimalist approach in transferring genera and creating new names and combinations.Consequently,we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus,Ampulloclitocybe andCantharocybe,despite weak phylogenetic support.We include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are lacking.The lower hygrophoroid clade is basal to Hygrophoraceae s.s.,comprising the genera Aphroditeola,Macrotyphula,Phyllotopsis,Pleurocybella,Sarcomyxa,Tricholomopsis and Typhula.

Taxonomy of Pseudolagarobasidium(Polyporales,Basidiomycota)

Pseudolagarobasidium(Polyporales,Basidiomycota)is a small,monophyletic genus of crustose,wood-inhabiting fungi with spines and a saprobic,endophytic,or parasitic habit.Seven species are accepted in the genus including two new species,P.belizense from Belize and P.pusillum from Australia.Sequence analysis of the internal transcribed spacer of the ribosomal RNA gene places P.belizense in a monophyletic clade with P.acaciicola and an undescribed foliar endophyte.New combinations proposed include P.modestum for Irpex modestus Berk.,P.pronum for Hydnum pronum Berk.&Broome which is an earlier name for P.calcareum,and P.venustum for Radulodon venustus Hjortstam&Ryvarden.Irpex colliculosum Berk.&Broome from Sri Lanka is conspecific with P.subvinosum.Two species,Sistotrema ochroleucum and Radulum concentricum are not accepted in Pseudolagarobasidium.Pseudolagarobasidium is compared with Radulodon and similar genera.A key to the species of Pseudolagarobasidium is provided.