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Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes

Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes

Armitage, Andrew ORCID: 0000-0002-0610-763X, Cockerton, Helen M., Sreenivasaprasad, Surapareddy, Woodhall, James, Lane, Charles R., Harrison, Richard J. and Clarkson, John P. (2020) Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes. Frontiers in Microbiology, 10:3124. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2019.03124)

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Abstract

The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotrophs, 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.

Item Type: Article
Additional Information: Copyright © 2020 Armitage, Cockerton, Sreenivasaprasad, Woodhall, Lane, Harrison and Clarkson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Uncontrolled Keywords: CDC, host-specific toxin, mating type, Dothideomycetes, Alternaria mali, Alternaria gaisen, nanopore
Subjects: S Agriculture > S Agriculture (General)
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department
Last Modified: 03 Mar 2020 17:30
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
URI: http://gala.gre.ac.uk/id/eprint/27097

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