Fungal species concepts in the genomics era

Abstract

The 140 000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.

Fusarium Species and Fusarium oxysporum Species Complex Genotypes Associated With Yam Wilt in South-Central China

“…For example, our SSR population genetic data are supportive F. aff. gossypinum as a new species within FOSC, consistent with the genotypic species concept (Xu, 2020). However, strains of F. aff.…”

“…Furthermore, both the allelic association analyses and the STRUCTURE analyses indicated allelic sharing at the six SSR loci and evidence for genetic exchanges at the population level among the species within FOSC. Thus, caution is needed in calling different genotypes as different species and more evidence should be gathered, preferably based on whole genome sequences, before further division of the FOSC into additional new species are proposed (Xu et al, 2016;Xu, 2020).…”

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

“…Different reference databases can yield widely different classification results for biological data, but standards are lacking to objectively assess the quality of individual databases [43]. Revisions to taxonomic naming [44][45][46][47][48][49] and the rapid pace at which new sequences and genomes are added to public databases mean that curated reference releases may lag behind [50]. Additionally, issues with amplicon length and sequence heterogeneity can limit the ability to identify species, especially from short marker-gene sequences or metagenome fragments [51].…”

Molecular Diagnostics and Detection of Oomycetes on Fiber Crops

“…Together, it is estimated that globally, there are 1.5 million species of plant pathogens with most still undescribed. Among the 140,000 or so described fungal species so far [2], around 20% are plant pathogens, and together, fungal pathogens cause 70-80% of all plant diseases [3]. Given the right ecological conditions, most plant pathogens can reproduce rapidly and have the potential to cause large-scale disease outbreaks in a short time.…”