Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation
ABSTRACT Phytophthora is a genus of oomycetes that includes many aggressive pathogens capable of devastating farmlands and forests worldwide. Among the oldest and most well‐known species, P. cactorum exhibits morphological and genetic similarities to other homothallic species within subclade 1a, whi...
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Wiley
2025-03-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.71105 |
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| author | Tao Lin Huiqin Wang Haiting Ma Jiaying Duan Wenxin Wang Xiaoyu Shi Yaling Li Zengqiang Qian Nian Liu Jiabin Zou Ayaka Hieno Koji Kageyama Mingzhu Li |
| author_facet | Tao Lin Huiqin Wang Haiting Ma Jiaying Duan Wenxin Wang Xiaoyu Shi Yaling Li Zengqiang Qian Nian Liu Jiabin Zou Ayaka Hieno Koji Kageyama Mingzhu Li |
| author_sort | Tao Lin |
| collection | DOAJ |
| description | ABSTRACT Phytophthora is a genus of oomycetes that includes many aggressive pathogens capable of devastating farmlands and forests worldwide. Among the oldest and most well‐known species, P. cactorum exhibits morphological and genetic similarities to other homothallic species within subclade 1a, which complicates the understanding of their evolutionary relationships. This study primarily compared seven P. cactorum strains from diverse origins with three closely related species in subclade 1a, utilizing mitogenome sequences for analysis. The circular mitogenomes of the four species were nearly identical in size and comprised 38 protein‐coding genes (PCGs), 25 transfer ribonucleic acid genes, and 2 ribosomal RNA genes. The mitochondrial genomes exhibited a higher percentage of A/T compared to G/C content. The majority of AT‐skew and GC‐skew values among the 38 PCGs were positive, with the AT‐skew demonstrating a more pronounced bias than the GC‐skew. The Ka/Ks ratios revealed that 35 PCGs underwent significant purifying selection. Although the AliGROOVE analysis indicated notable similarities among the subclade 1a species, four PCGs exhibited significantly higher pairing frequency compared to the complete mitogenome. The results from the phylogenetic analysis aligned with the pairwise genetic distances, indicating that P. cactorum is more closely related to P. pseudotsugae than to P. hedraiandra. Furthermore, we found that the nad9 gene is informative to differentiate closely related Phytophthora species within subclade 1a, akin to the cox1 gene. |
| format | Article |
| id | doaj-art-824f087b201b4d538e2bfccb600fba90 |
| institution | OA Journals |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-824f087b201b4d538e2bfccb600fba902025-08-20T02:14:01ZengWileyEcology and Evolution2045-77582025-03-01153n/an/a10.1002/ece3.71105Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their DifferentiationTao Lin0Huiqin Wang1Haiting Ma2Jiaying Duan3Wenxin Wang4Xiaoyu Shi5Yaling Li6Zengqiang Qian7Nian Liu8Jiabin Zou9Ayaka Hieno10Koji Kageyama11Mingzhu Li12The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaCollege of Life Sciences, Shaanxi Normal University Xi'an ChinaRiver Basin Research Center Gifu University Gifu JapanRiver Basin Research Center Gifu University Gifu JapanThe Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education Shaanxi Normal University Xi'an ChinaABSTRACT Phytophthora is a genus of oomycetes that includes many aggressive pathogens capable of devastating farmlands and forests worldwide. Among the oldest and most well‐known species, P. cactorum exhibits morphological and genetic similarities to other homothallic species within subclade 1a, which complicates the understanding of their evolutionary relationships. This study primarily compared seven P. cactorum strains from diverse origins with three closely related species in subclade 1a, utilizing mitogenome sequences for analysis. The circular mitogenomes of the four species were nearly identical in size and comprised 38 protein‐coding genes (PCGs), 25 transfer ribonucleic acid genes, and 2 ribosomal RNA genes. The mitochondrial genomes exhibited a higher percentage of A/T compared to G/C content. The majority of AT‐skew and GC‐skew values among the 38 PCGs were positive, with the AT‐skew demonstrating a more pronounced bias than the GC‐skew. The Ka/Ks ratios revealed that 35 PCGs underwent significant purifying selection. Although the AliGROOVE analysis indicated notable similarities among the subclade 1a species, four PCGs exhibited significantly higher pairing frequency compared to the complete mitogenome. The results from the phylogenetic analysis aligned with the pairwise genetic distances, indicating that P. cactorum is more closely related to P. pseudotsugae than to P. hedraiandra. Furthermore, we found that the nad9 gene is informative to differentiate closely related Phytophthora species within subclade 1a, akin to the cox1 gene.https://doi.org/10.1002/ece3.71105mitogenomeP. Cactorum complexphylogenyPhytophthora |
| spellingShingle | Tao Lin Huiqin Wang Haiting Ma Jiaying Duan Wenxin Wang Xiaoyu Shi Yaling Li Zengqiang Qian Nian Liu Jiabin Zou Ayaka Hieno Koji Kageyama Mingzhu Li Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation Ecology and Evolution mitogenome P. Cactorum complex phylogeny Phytophthora |
| title | Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation |
| title_full | Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation |
| title_fullStr | Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation |
| title_full_unstemmed | Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation |
| title_short | Evolutionary Relationships of the Phytophthora 1a Subclade Species Based on Complete Mitogenomes, and Novel Markers for Their Differentiation |
| title_sort | evolutionary relationships of the phytophthora 1a subclade species based on complete mitogenomes and novel markers for their differentiation |
| topic | mitogenome P. Cactorum complex phylogeny Phytophthora |
| url | https://doi.org/10.1002/ece3.71105 |
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