Fungal endophytes in green coffee seeds

Green coffee seeds from Colombia, Guatemala, India, Kenya, Papua New Guinea, Puerto Rico and Vietnam were sampled for the presence of fungal endophytes. Stions of surface sterilized seeds were plated on yeast malt agar, and fungal growth was isolated for subsequent DNA extraction and sequencing. Several fungal genera were isolated, including Acremonium, Aspergillus, Eurotium, Fusarium, Gibberella, Penicillium, Pseudozyma and an undescribed clavicipitaceous species. The biological activities that these fungi might be playing in coffee seeds remain unknown, but in other plants some of the genera isolated have been reported to protect against plant pathogens.

Tubeufiales,ord.nov.,integrating sexual and asexual generic names

Tubeufiaceae is based on the generic type Tubeufia,which is characterized by superficial,oval and bright ascomata,bitunicate asci,mostly long fusiform to filiform,transeptate ascospores and hyphomycetous asexual states with helicosporous conidia.Most species in this family are saprobic on terrestrial woody substrates and some are aquatic.Their distinct morphology as well as combined LSU,SSU and TEF1 sequence analysis show that Tubeufiaceae should be accommodated in a new order Tubeufiales,which is introduced in this paper.Phylogenetic analyses of combined LSU and ITS sequences were used to resolve genera and species within the family Tubeufiaceae.In this study,we examine and incorporate sexual and asexual states of genera in Tubeufiales to provide a modern treatment,based on single names.An epitype for Tubeufia javanica,the type species of Tubeufia,is designated and represents Tubeufia sensu stricto.The genera Acanthophiobolus,Acanthostigma,Boerlagiomyces,Chlamydotubeufia,Kamalomyces,Podonectria,Thaxteriella and Thaxteriellopsis are accepted,Acanthostigmina is reinstated,and the asexual genera Aquaphila,Helicoma,Helicomyces,Helicosporium and Tamhinispora are accepted in Tubeufiaceae.Three new genera Acanthohelicospora,Helicangiospora and Neoacanthostigma are introduced.The genus Bifrontia is added to the family based on morphological similarity.The incongruous morphological genera Acanthostigmella,Amphinectria,Chaetocrea,Chaetosphaerulina,Glaxoa,Malacaria,Melioliphila,Paranectriella,Puttemansia,Rebentischia and Uredinophila are excluded from Tubeufiaceae despite having characteristic ascomata with setae and multiseptate long spores.A key to genera accepted in Tubeufiaceae is provided.

The genus Thelonectria(Nectriaceae,Hypocreales,Ascomycota)and closely related species with cylindrocarpon-like asexual states

The genus Thelonectria and closely related species with cylindrocarpon-like asexual states are a group of perithecial ascomycetes in the family Nectriaceae that occur as saprobes and in few cases as pathogens of hardwood trees,shrubs or other plants.Although a key component of forest ecosystems around the world,species relationships and distributions of these fungi are largely unknown.The objectives of this study were to:1)infer species rank phylogenetic relationships of the genus Thelonectria and closely related species with cylindrocarpon-like asexual states and test the monophyly of each of the groups studied;2)delimit taxa establishing taxon circumscriptions;3)resolve nomenclatural issues by identifying redundantly used names and synonyms;and 4)provide an updated outline to the genus,geographical distributions data and identification tools,specifically diagnostic keys and molecular data that can be used as molecular barcodes.The recovered consensus phylogeny resulted in a narrow circumscription of the genus Thelonectria,based on the type T.discophora,excluding one of the common species T.jungneri.According to the phylogenetic analyses,T.jungneri belongs in a segregate clade that should be recognized as a different genus.In the genus Thelonectria,a total of four new species and three new combinations are recognized.Additionally,three new genera,closely related to Thelonectria,are described to accommodate species displaying a morphological resemblance to those of Thelonectria:Cinnamomeonectria gen.nov.with C.cinnamomea as type species,Macronectria gen.nov.with M.jungneri as type species and including four additional newly described species,and Tumenectria gen.nov.with T.laetidisca as type species.

Phylogeny and taxonomic revision of Thelonectria discophora(Ascomycota,Hypocreales,Nectriaceae)species complex

Specimens regarded as Thelonectria discophora(Thelonectria,Nectriaceae,Hypocreales)constitute a conspicuous group of saprobic fungi on decaying plant material,characterized by red perithecia each with a broad mammiform(nipple-like)apex.The asexual state is characterized by a cylindrocarpon-like morphology,with 3–5 septate macroconidia,unicellular microconidia and chlamydospores that are rarely produced in culture.In the past,T.discophora was regarded as one species with a wide geographic distribution.However,a recent study rejected the monophyly and cosmopolitan distribution of this species,and showed the existence of at least 16 cryptic species distributed in three main groups.By combining the results of phylogenetic analyses of six nuclear loci and morphological studies,we revised the taxonomy of the T.discophora species complex,resulting in the description of 12 new species and four new combinations based on historic names.Even though molecular phylogenetic analyses strongly support the segregation of these species,and are in agreement with previous studies,individual diagnostic morphological characters for each species could not be identified.However,discrete morphological traits corresponding to each of the three main groups of species were discovered.Lineages could be differentiated based on the average values of morphological traits as well as the presence/absence of characteristic asexual propagules and colony growth at 30C.Descriptions,illustrations are provided for the recognized species.

Insights into the genus Diaporthe:phylogenetic species delimitation in the D.eres species complex

The genus Diaporthe comprises pathogenic,endophytic and saprobic species with both temperate and tropical distributions.Cryptic diversification,phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus.The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures.Species limits of D.eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer(ITS),partial sequences of actin(ACT),DNA-lyase(Apn2),translation elongation factor 1-α(EF1-α),beta-tubulin(TUB),calmodulin(CAL),60s ribosomal protein L37(FG1093)and histone-3(HIS).The occurrence of sequence heterogeneity of ITS within D.eres is observed,which complicates the analysis and may lead to overestimation of the species diversity.The strict criteria of Genealogical Concordance Phylogenetic Species Recognition(GCPSR)were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS.We accept nine distinct phylogenetic species including Diaporthe alleghaniensis,D.alnea,D.bicincta,D.celastrina,D.eres,D.helicis,D.neilliae,D.pulla and D.vaccinii.Epitypes are designated for D.alnea,D.bicincta,D.celastrina,D.eres,D.helicis and D.pulla.Modern descriptions and illustrations are provided for these species.Newly designed primers are introduced to amplify and sequence the Apn2(DNA-lyase)gene in Diaporthe.Based on phylogenetic informativeness profiles,EF1-α,Apn2 and HIS genes are recognised as the best markers for defining species in the D.eres complex.

含亚洲、欧洲、北美洲山毛榉病害病原菌的Neonectria coccinea复合群的物种概念

对包含亚洲、欧洲、北美洲山毛榉病害病原菌在内的Neonectria coccinea复合群中物种之间的系统演化关系以及物种概念进行了探讨。Neonectria faginata(曾处理为Neo.coccinea var.faginata)与狭义的Neo.coccinea和Neo.punicea有明显区别。系统树显示5个分支与Neo.coccinea群的关系较为接近,由于缺乏显著的形态差异,它们始终没有在物种的等级上区分。根据形态学、系统发育、寄主专化性和地理因素,采用多基因act、ITS、LSU、rpb1、tef1和tub序列分析的方法,对亚洲、欧洲、北美洲的相关材料进行了研究,结果表明,它们代表4个独立的物种,即Neo.coccinea,Neo.faginata,Neo.microconidia和Neo.punicea,对每个种进行了详尽的描述和图示。并为Sphaeria coccinea和Neonectria coccinea var.faginata指定了附加模式。

Corallomycetella属及以C. jatrophae为模式建立新属Corallonectria(丛赤壳科,肉座菌目)(英文)

对Corallomycetella属的概念进行了阐述,该属包括子实体为红色、在自然和培养条件下产生菌索的丛赤壳类真菌。根据对近期采集的标本的观察和多基因系统树分析的结果,广义的Corallomycetella repens形成2个分支,它们与生物地理因素相关联。狭义的Corallomycetella repens限于来自亚洲的标本,而C.elegans来自非洲和美洲。Corallomycetella属成熟的子囊孢子表面具有纤细条纹,此特征过去曾被忽略,C.jatrophae与广义的Neonectria属关系接近,而与C.repens和C.elegans关系较远;因而建立新属Corallonectria,其子囊壳表面细粉状,无性型为束丝结构并与镰孢菌相似。