Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry
Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. T...
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1214924/full |
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| author | Anupam Gogoi Anupam Gogoi Simeon L. Rossmann Erik Lysøe Arne Stensvand Arne Stensvand May Bente Brurberg May Bente Brurberg |
| author_facet | Anupam Gogoi Anupam Gogoi Simeon L. Rossmann Erik Lysøe Arne Stensvand Arne Stensvand May Bente Brurberg May Bente Brurberg |
| author_sort | Anupam Gogoi |
| collection | DOAJ |
| description | Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4–67.6 megabases genomes in 178–204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry. |
| first_indexed | 2024-03-13T01:46:44Z |
| format | Article |
| id | doaj.art-9115c42f912f482ba97fbc47fdc315d5 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-13T01:46:44Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-9115c42f912f482ba97fbc47fdc315d52023-07-03T08:04:14ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-07-011410.3389/fmicb.2023.12149241214924Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberryAnupam Gogoi0Anupam Gogoi1Simeon L. Rossmann2Erik Lysøe3Arne Stensvand4Arne Stensvand5May Bente Brurberg6May Bente Brurberg7Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, NorwayDivision of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, NorwayDivision of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, NorwayDivision of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, NorwayDepartment of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, NorwayDivision of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, NorwayDepartment of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, NorwayDivision of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, NorwayPhytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4–67.6 megabases genomes in 178–204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1214924/fulloomycetePacBio sequel II sequencingelicitorsRxLRsCrinklerseffectors |
| spellingShingle | Anupam Gogoi Anupam Gogoi Simeon L. Rossmann Erik Lysøe Arne Stensvand Arne Stensvand May Bente Brurberg May Bente Brurberg Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry Frontiers in Microbiology oomycete PacBio sequel II sequencing elicitors RxLRs Crinklers effectors |
| title | Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry |
| title_full | Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry |
| title_fullStr | Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry |
| title_full_unstemmed | Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry |
| title_short | Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry |
| title_sort | genome analysis of phytophthora cactorum strains associated with crown and leather rot in strawberry |
| topic | oomycete PacBio sequel II sequencing elicitors RxLRs Crinklers effectors |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1214924/full |
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