Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation
Abstract Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and 8. kuwatsukai. Here, we sequenced the genomes of 8. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and 8. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat...
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | IMA Fungus |
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| Online Access: | http://link.springer.com/article/10.5598/imafungus.2018.09.02.02 |
| _version_ | 1826841263175892992 |
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| author | Bo Wang Xiaofei Liang Mark L. Gleason Rong Zhang Guangyu Sun |
| author_facet | Bo Wang Xiaofei Liang Mark L. Gleason Rong Zhang Guangyu Sun |
| author_sort | Bo Wang |
| collection | DOAJ |
| description | Abstract Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and 8. kuwatsukai. Here, we sequenced the genomes of 8. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and 8. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g.carbohydrateactive enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in 8. dothidea and 8. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security. |
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| language | English |
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| spelling | doaj.art-f5d08723acb54ac79b2a94166117c74d2025-02-02T18:13:40ZengBMCIMA Fungus2210-63592018-12-019224325710.5598/imafungus.2018.09.02.02Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciationBo Wang0Xiaofei Liang1Mark L. Gleason2Rong Zhang3Guangyu Sun4State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, YanglingState Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, YanglingDepartment of Plant Pathology and Microbiology, Iowa State UniversityState Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, YanglingState Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, YanglingAbstract Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and 8. kuwatsukai. Here, we sequenced the genomes of 8. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and 8. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g.carbohydrateactive enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in 8. dothidea and 8. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.http://link.springer.com/article/10.5598/imafungus.2018.09.02.02genome sequencingvirulence factorspathogenicityBotryosphaeriaceaegenome evolution |
| spellingShingle | Bo Wang Xiaofei Liang Mark L. Gleason Rong Zhang Guangyu Sun Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation IMA Fungus genome sequencing virulence factors pathogenicity Botryosphaeriaceae genome evolution |
| title | Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation |
| title_full | Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation |
| title_fullStr | Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation |
| title_full_unstemmed | Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation |
| title_short | Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation |
| title_sort | comparative genomics of botryosphaeria dothidea and b kuwatsukai causal agents of apple ring rot reveals both species expansion of pathogenicity related genes and variations in virulence gene content during speciation |
| topic | genome sequencing virulence factors pathogenicity Botryosphaeriaceae genome evolution |
| url | http://link.springer.com/article/10.5598/imafungus.2018.09.02.02 |
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