Secondary DNA Barcodes (CAM, GAPDH, GS, and RpB2) to Characterize Species Complexes and Strengthen the Powdery Mildew Phylogeny

Abstract

Powdery mildews are a group of economically and ecologically important plant pathogens. In the past 25 years the use of ribosomal DNA (rDNA) in the powdery mildews has led to major taxonomic revisions. However, the broad scale use of rDNA has also revealed multiple species complexes that cannot be differentiated based on ITS + LSU data alone. Currently, there are only two powdery mildew taxonomic studies that took a multi-locus approach to resolve a species complex. In the present study, we introduce primers to sequence four additional regions (CAM, GAPDH, GS, and RPB2) that have the potential to improve support values in both broad and fine scale phylogenetic analyses. The primers were applied to a broad set of powdery mildew genera in China and the United States, and phylogenetic analyses included some of the common complexes. In taxa with nearly identical ITS sequences the analyses revealed a great amount of diversity. In total 154 non-rDNA sequences from 11 different powdery mildew genera were deposited in NCBI’s GenBank, laying the foundation for secondary barcode databases for powdery mildews. The combined and single loci phylogenetic trees constructed generally followed the previously defined species/genus concepts for the powdery mildews. Future research can use these primers to conduct in depth phylogenetic, and taxonomic studies to elucidate the evolutionary relationships of species and genera within the powdery mildews.

More Than Just Plants: Botanical Gardens Are an Untapped Source of Fungal Diversity

“…Species of 18 out of the 19 powdery mildew genera are represented, and Arachnopeziza was used as an outgroup based on the analysis by Johnston et al (2019). A maximum clade credibility tree was constructed using Bayesian analyses of the sequences by and Bradshaw et al (2022c). Thicker lines indicate higher posterior probabilities.…”

“…Phylogeny. A concatenated GAPDH-CAM-GS-ITS-LSU-RPB2 tree was constructed based on the sequences and analyses of and Bradshaw et al (2022c). Sequences were aligned and edited using MUSCLE in MEGA11: Molecular Evolutionary Genetics Analysis version 11 (Tamura et al, 2021).…”

Identification, pathogenicity and control of powdery mildew caused by Erysiphe elevata on Eucalyptus pellita in Sumatra, Indonesia

“…The phylogeny and taxonomy of Erysiphe elevata , including records on Eucalyptus spp., are not yet fully clarified. Sequences of ITS+28S retrieved from E. elevata and E. vaccinii are indistinguishable (Bradshaw et al, 2022; Tymon et al, 2022). A multilocus approach is needed.…”

“…In the Erysiphaceae, the most studied DNA regions are ITS and 28S rDNA (Braun & Cook, 2012; Glawe, 2008), and the lack of available information about other genetic regions hampers fungal classifications, especially for those species not easily forming the sexual morph. Other DNA regions commonly used for taxonomic studies are beta‐tubulin and translation elongation factor, recently supplemented by CAM, GAPDH, GS and RpB2 (Bradshaw et al, 2022), but amplifications of other member of Erysiphaceae occurring on eucalypt were unsuccessful when tested elsewhere (Fonseca et al, 2017). In our study, sequencing of ITS region was successfully performed and helped to characterize the isolates of Erysiphe elevata occurring in Sumatra, Indonesia.…”

Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

“…Two additional commonly used loci are transcription enhancer factor 1α and β-tubulin (Bruns et al, 1991; Hibbett et al, 2016; Raja et al, 2017; Lücking et al, 2021). Secondary barcodes are also often used to characterize species complexes (Bradshaw et al, 2022)—such as calmodulin for Aspergillus and other species (Susca et al, 2020)—owing to the power of more loci in phylogenetic reconstructions.…”