AlternariasectionAlternaria: Species,formae specialesor pathotypes?

Abstract

The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternaria have 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. Alternaria are supported by molecular data, whole-genome sequencing of nine Alternaria morphospecies supplemented with transcriptome sequencing of 12 Alternaria morphospecies as well as multi-gene sequencing of 168 Alternaria isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. Alternaria and from 32.0–39.1 Mb for all Alternaria genomes. The number of repetitive sequences differed significantly between the different Alternaria genomes; ranging from 1.4–16.5 %. The repeat content within sect. Alternaria was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. Alternaria isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the A. alternata reference 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 the A. alternata reference 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. Alternaria was tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPG and 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. Alternaria more effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternaria sect. Alternaria, this manuscript provides a clear and st...

Mycosphere notes 1-50: Grass (Poaceae) inhabiting Dothideomycetes

“…Colonies growing on PDA, reaching a diameter of 40 mm after 7 d at 25 °C, flat to slightly umbonate, surface velvety, with entire to slightly undulate edge, grey, dense, circular to slightly irregular; reverse orange buff to greyish. Notes -Alternaria longipes is commonly known as the causal agent of brown spot of tobacco (Nicotiana tabacum) and widely distributed in U.S.A. (Woudenberg et al 2015). During our research, we found this species on Triticum aestivum L. from China and the present phylogenetic analysis confirms its identity (Fig.…”

“…Notes -Alternaria alternata belongs to the Alternaria sect. Alternaria, which consists of only eleven phylogenetic species and one species complex (Woudenberg et al 2015). Woudenberg et al (2015) listed many synonyms under A. alternata based on genome and transcriptome comparisons and molecular phylogenies.…”

“…Alternaria, which consists of only eleven phylogenetic species and one species complex (Woudenberg et al 2015). Woudenberg et al (2015) listed many synonyms under A. alternata based on genome and transcriptome comparisons and molecular phylogenies. Alternaria alternata occurs on a number of substrates worldwide and we collected the species associated with Sorghum bicolor (L.) Conrad Moench,769 Triticum aestivum L., and bamboo sp.…”

Diversity among Isolates of the Tangerine Pathotype of <i>Alternaria alternata</i>

“…There are more than eleven new species of Alternaria described as causal agents of the brown spot in different parts of the world, however, due to the conflicting morphological data, molecular studies have been expanded through polymorphism sequencing and mitochondrial restriction fragment length DNA and regions internally transcribed in the ribosome, where it has favored the identification of the close phylogenetic relationship between the isolates producing toxins and ensuring the establishment of identity as well as its variability [11].…”

“…Indeed, environmental conditions are a major cause of genetic variation within a population and exert an influence on the emergence of new genotypes and new combinations involving the fusion of gametes, the recombination of alleles during the pairing of homologous chromosomes, segregation and the generation of viable descendants [11].…”