Alternaria section Alternaria: Species, formae speciales or pathotypes?

The cosmopolitan fungal genusAlternariaconsists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections.Alternariasect.Alternariacontains most of the small-sporedAlternariaspecies with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect.Alternariahave been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect.Alternariaare supported by molecular data, whole-genome sequencing of nineAlternariamorphospecies supplemented with transcriptome sequencing of 12Alternariamorphospecies as well as multi-gene sequencing of 168Alternariaisolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect.Alternariaand from 32.0–39.1 Mb for allAlternariagenomes. The number of repetitive sequences differed significantly between the differentAlternariagenomes; ranging from 1.4–16.5 %. The repeat content within sect.Alternariawas relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect.Alternariaisolates, compared to 85.1–89.3 % genome identity for isolates from other sections to theA. alternatareference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect.Alternaria, while the percentage of SNPs found in isolates from different sections compared to theA. alternatareference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect.Alternaria(96.8 and 97.3 % conservation). Their potential discriminatory power within sect.Alternariawas tested next to nine commonly used gene regions in sect.Alternaria, namely the SSU, LSU, ITS,gapdh,rpb2,tef1,Alt a 1,endoPGand OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect.Alternariamore effectively than the phylogenies based on the commonly used gene regions forAlternaria. Based on genome and transcriptome comparisons and molecular phylogenies,Alternariasect.Alternariaconsists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised underA. alternata. By providing guidelines for the naming and identification of phylogenetic species inAlternariasect.Alternaria, this manuscript provides a clear and stable species classification in this section.