Revision of <i>Alternaria</i> sections <i>Pseudoulocladium</i> and <i>Ulocladioides</i>: Assessment of species boundaries, determination of mating-type loci, and identification of Russian strains

<i>Alternaria</i> is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including <i>Ulocladium</i>. The majority of <i>Ulocladium</i> species after incorporation into <i>Alternaria</i> were placed in three sections: <i>Ulocladioides, Pseudoulocladium</i>, and <i>Ulocladium</i>. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian <i>Ulocladium</i>-like isolates was recovered. The partial actin gene (<i>act</i>), <i>Alternaria</i> major allergen (<i>alta1</i>), calmodulin (<i>cal</i>), glyceraldehyde-3-phosphate dehydrogenase (<i>gapdh</i>), RNA polymerase II second largest subunit (<i>rpb2</i>), and translation elongation factor 1-α (<i>tef1</i>) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the <i>Pseudoulocladium</i> and <i>Ulocladioides</i> sections. The <i>Pseudoulocladium</i> clade included four reference strains and nine local isolates and considered to be a single species, whereas the <i>Ulocladioides</i> section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species <i>A. atra</i> and <i>A. multiformis</i> were combined into the single species <i>A. atra</i>. Five species, <i>A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea</i>, and <i>A. terricola</i>, were united in the species <i>A. consortialis. Alternaria heterospora</i> and <i>A. subcucurbitae</i> were combined into one species, <i>A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata</i>, and <i>A. septospora</i> were combined into a single species, <i>A. chartarum</i>. Also, amplification with two different primer sets was performed to define mating-type locus 1 (<i>MAT1</i>) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian <i>Ulocladium</i>-like isolates were assigned to five species of two sections, <i>A. atra, A. cantlous, A. chartarum, A. consortialis</i>, and <i>A. subcucurbitae</i>. Species <i>A. cantlous</i> and <i>A. subcucurbitae</i> were found in Russia for the first time.