A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

The genus Diaporthe(Phomopsis)includes important plant pathogenic fungi with wide host ranges and geographic distributions.In the present study,phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS,and partial sequences from the translation elongation factor 1-α(EF 1-α),βtubulin(TUB)and calmodulin(CAL)molecular markers.DNA sequences of available extype cultures have been included,providing a multi-locus backbone tree for future studies on Diaporthe.Four utilizable loci were analyzed individually and in combination,and ITS,EF 1-αand multi-locus phylogenetic trees are presented.The phylogenetic tree inferred by combined analysis of four loci provided the best resolution for species as compared to single gene analysis.Notes are provided for nine species previously known in Phomopsis that are transferred to Diaporthe in the present study.The unraveling of cryptic species complexes of Diaporthe based on Genealogical Concordance Phylogenetic Species Recognition(GCPSR)is emphasized.

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.

Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics

Early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyletic genera.Although some taxonomic confusion in the family has been clarified,rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae.In this study,we applied two parallel approaches to resolve the Mortierel-laceae phylogeny:low coverage genome(LCG)sequencing and high-throughput,multiplexed targeted amplicon sequenc-ing to generate sequence data for multi-gene phylogenetics.We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset.Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera,7 of which are newly proposed.Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny.The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach,but has limitations too.We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.