Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes
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 gro...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.03124/full |
| _version_ | 1819315570603982848 |
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| author | Andrew D. Armitage Andrew D. Armitage Helen M. Cockerton Surapareddy Sreenivasaprasad James Woodhall Charles R. Lane Richard J. Harrison John P. Clarkson |
| author_facet | Andrew D. Armitage Andrew D. Armitage Helen M. Cockerton Surapareddy Sreenivasaprasad James Woodhall Charles R. Lane Richard J. Harrison John P. Clarkson |
| author_sort | Andrew D. Armitage |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-24T10:02:13Z |
| format | Article |
| id | doaj.art-544a3dfba116435eb3d5bc693da6b3c2 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-24T10:02:13Z |
| publishDate | 2020-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-544a3dfba116435eb3d5bc693da6b3c22022-12-21T17:01:00ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-01-011010.3389/fmicb.2019.03124462591Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear PathotypesAndrew D. Armitage0Andrew D. Armitage1Helen M. Cockerton2Surapareddy Sreenivasaprasad3James Woodhall4Charles R. Lane5Richard J. Harrison6John P. Clarkson7NIAB EMR, East Malling, United KingdomNatural Resources Institute, University of Greenwich, Chatham Maritime, London, United KingdomNIAB EMR, East Malling, United KingdomSchool of Life Sciences, University of Bedfordshire, Luton, United KingdomParma Research and Extension Center, University of Idaho, Parma, ID, United StatesFERA Science Ltd., York, United KingdomNIAB EMR, East Malling, United KingdomWarwick Crop Centre, University of Warwick, Warwick, United KingdomThe 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.https://www.frontiersin.org/article/10.3389/fmicb.2019.03124/fullCDChost-specific toxinmating typeDothideomycetesAlternaria maliAlternaria gaisen |
| spellingShingle | Andrew D. Armitage Andrew D. Armitage Helen M. Cockerton Surapareddy Sreenivasaprasad James Woodhall Charles R. Lane Richard J. Harrison John P. Clarkson Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes Frontiers in Microbiology CDC host-specific toxin mating type Dothideomycetes Alternaria mali Alternaria gaisen |
| title | Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes |
| title_full | Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes |
| title_fullStr | Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes |
| title_full_unstemmed | Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes |
| title_short | Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes |
| title_sort | genomics evolutionary history and diagnostics of the alternaria alternata species group including apple and asian pear pathotypes |
| topic | CDC host-specific toxin mating type Dothideomycetes Alternaria mali Alternaria gaisen |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.03124/full |
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