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

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Armitage, Andrew D., 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. doi:10.3389/fmicb.2019.03124

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Official URL: http://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 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.

Item Type: Journal Article
Subjects: Q Science > QC Physics
Q Science > QH Natural history
Q Science > QK Botany
Q Science > QR Microbiology
S Agriculture > SB Plant culture
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
SWORD Depositor: Library Publications Router
Library of Congress Subject Headings (LCSH): Chromosomes, Plant-pathogen relationships , Plant-microbe relationships, Dothideomycetes, Alternaria , Nanopores
Journal or Publication Title: Frontiers in Microbiology
Publisher: Frontiers Media S.A.
ISSN: 1664-302X
Official Date: 23 January 2020
Dates:
DateEvent
23 January 2020Published
24 December 2019Accepted
Volume: 10
Article Number: 3124
DOI: 10.3389/fmicb.2019.03124
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
Plant Health Taxonomic fellowship 2010–2014Department for Environment, Food and Rural Affairshttp://dx.doi.org/10.13039/501100000277
BB/K017071/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/K020730/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268

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