Abstract
The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.
Highlights
Species within the genus Alternaria encompass a range of lifestyles, acting as saprotroph, opportunistic pathogens, and host-adapted plant pathogens (Thomma, 2003)
We report near-complete reference genomes for the apple and Asian pear pathotypes of A. sect. alternaria and provide genomic resources for a further ten diverse isolates from this clade
For the first time we show sequenced Alternaria genomes in a phylogenetic context allowing the identification of both mating type idiomorphs present in A. arborescens and A. tenuissima, with a distribution throughout subclades that was indicative of recent genetic exchange
Summary
Species within the genus Alternaria encompass a range of lifestyles, acting as saprotroph, opportunistic pathogens, and host-adapted plant pathogens (Thomma, 2003). Genomic Characterization of Alternaria in the environment acting as saprotrophs and opportunistic necrotrophs This species group is responsible for opportunistic human infections and a range of host adapted plant diseases. Taxonomy within this presumed asexual genus has been subject to recent revision (Lawrence et al, 2013). Small spored species within the A. alternata species group overlap in morphological characters, possess the same ITS haplotype (Kusaba and Tsuge, 1995), and show low variation in other commonly used barcoding markers (Lawrence et al, 2013; Armitage et al, 2015; Woudenberg et al, 2015). Variable phylogenetic markers have provided resolution between groups of isolates that possess morphological patterns typical of descriptions for Alternaria gaisen, Alternaria tenuissima, and Alternaria arborescens (Armitage et al, 2015)
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