Species in Alternaria sections Infectoriae and Pseudoalternaria are commonly isolated from agri-cultural crops and a variety of other plant hosts. With the increasing appreciation that species from these two sections are often the dominant taxa recovered from important cereal crops, the need for improved understanding of their biodiversity and taxonomy has grown. Given that morphological characteristics and existing molecular markers are not sufficient for distinguishing among species, we expanded the genomic resources for these sections to support research in biosystematics and species diagnostics. Whole genome assemblies for 22 strains were generated, including the first genomes from section Infectoriae or Pseudoalternaria strains sampled from Canada, which significantly increases the number of publicly released genomes, particularly for section Pseudoalternaria. We performed comprehensive phylogenomic analyses of all available genomes (n = 39) and present the first robust phylogeny for these taxa. The segregation of the two sections was strongly supported by genome wide data, and multiple lineages were detected within each section. We then provide an overview of the biosystematics of these groups by analyzing two standard molecular markers from the largest sample of section Infectoriae and Pseudoalternaria strains studied to date. The patterns of relative diversity suggest that, in many cases, multiple species described based on minor morphological differences may actually represent different strains of the same species. A list of candidate loci for development into new informative molecular markers, which are diagnostic for sections and lineages, was created from analyses of phylogenetic signals from individual genes across the entire genome.

Fourth, our analyses revealed that diversity among strains is similar to that for diversity among species that have been described based on minor morphological differences. This result suggests that, in many cases, the previously erected morphospecies may represent different strains from the same species.

According to Hong et al. (2005), the major allergen Alt a 1 facilitates identification to the species level, but later studies showed that it is not sufficient within some sections like the small-spored section Alternaria (Dettman & Eggertson, 2021; Hong et al., 2005; Woudenberg et al., 2015). When using molecular barcode markers, a combination of several loci is necessary. The most commonly used markers are ITS, GAPDH, RPB2, TEF1 and Alt a 1 (e.g., Kokaeva et al., 2022; Woudenberg et al., 2014), and most studies with a multilocus phylogeny employ these five or subset of them, with or without additional, less common loci like endoPG, histone H3, calmodulin and OPA 10–2 (e.g., Adhikari et al., 2020; Bessadat et al., 2021; Ding et al., 2019; Landschoot, Vandecasteele, Carrette, et al., 2017; Woudenberg et al., 2015). Recently, Dettman et al. developed (Dettman & Eggertson, 2021, 2022) and tested (Dettman et al., 2023) new markers to achieve better identification of small-spored Alternaria.

Nishikawa and Nakashima claim that morphological and molecular phylogenetic data should be complemented by experimental host ranges to achieve an integrated species recognition (Nishikawa & Nakashima, 2020). Genes for host-specific toxins are subject to horizontal gene transfer and some A. alternata pathotypes spontaneously lose their pathogenicity as a consequence of losing their capability to produce the host-specific toxin, so pathotype should not be employed as a character in the taxonomy of small-spored Alternaria (Andrew et al., 2009; Pinto & Patriarca, 2017). Chemotaxonomy, using secondary metabolite profiling for species identification, showed promising results for some species groups like A. infectoria (Andersen et al., 2008; Andersen & Thrane, 1996; Kelman et al., 2020; Zwickel et al., 2018) but not for all sections of Alternaria (Andersen et al., 2015; Zwickel et al., 2018). Secondary metabolite profiles can be combined with morphological and molecular analyses for polyphasic taxonomy (Pinto & Patriarca, 2017). The study by Woudenberg et al. (2015) is also an example for the combination of methodological approaches, as it employed a multilocus phylogeny, whole genome data and transcriptomics (Woudenberg et al., 2015).