High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia
The olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in th...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.879822/full |
| _version_ | 1828202584491425792 |
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| author | Li Wang Jianguo Zhang Jianguo Zhang Dan Peng Yang Tian Dandan Zhao Wanning Ni Jinhua Long Jinhua Li Yanfei Zeng Yanfei Zeng Zhiqiang Wu Yiyun Tang Zhaoshan Wang Zhaoshan Wang |
| author_facet | Li Wang Jianguo Zhang Jianguo Zhang Dan Peng Yang Tian Dandan Zhao Wanning Ni Jinhua Long Jinhua Li Yanfei Zeng Yanfei Zeng Zhiqiang Wu Yiyun Tang Zhaoshan Wang Zhaoshan Wang |
| author_sort | Li Wang |
| collection | DOAJ |
| description | The olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. europaea, which makes subsp. cuspidata a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. cuspidata with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, evm.model.Chr16.1133, was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the Cercospora genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. cuspidata and europaea. |
| first_indexed | 2024-04-12T11:50:44Z |
| format | Article |
| id | doaj.art-b056bafd91bd4396ac79dbbc1818cb19 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T11:50:44Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-b056bafd91bd4396ac79dbbc1818cb192022-12-22T03:34:11ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-05-011310.3389/fpls.2022.879822879822High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East AsiaLi Wang0Jianguo Zhang1Jianguo Zhang2Dan Peng3Yang Tian4Dandan Zhao5Wanning Ni6Jinhua Long7Jinhua Li8Yanfei Zeng9Yanfei Zeng10Zhiqiang Wu11Yiyun Tang12Zhaoshan Wang13Zhaoshan Wang14Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCollaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaKunpeng Institute of Modern Agriculture at Foshan, Foshan, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCollaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaKunpeng Institute of Modern Agriculture at Foshan, Foshan, ChinaEcological Restoration and Industrial Development Workstation, Nujiang State Forestry and Grassland Bureau of Yunnan Province, Kunming, ChinaKey Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCollaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaThe olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. europaea, which makes subsp. cuspidata a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. cuspidata with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, evm.model.Chr16.1133, was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the Cercospora genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. cuspidata and europaea.https://www.frontiersin.org/articles/10.3389/fpls.2022.879822/fullgenome assemblyOlea europaeasusceptibility genedemographic historynature selection |
| spellingShingle | Li Wang Jianguo Zhang Jianguo Zhang Dan Peng Yang Tian Dandan Zhao Wanning Ni Jinhua Long Jinhua Li Yanfei Zeng Yanfei Zeng Zhiqiang Wu Yiyun Tang Zhaoshan Wang Zhaoshan Wang High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia Frontiers in Plant Science genome assembly Olea europaea susceptibility gene demographic history nature selection |
| title | High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia |
| title_full | High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia |
| title_fullStr | High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia |
| title_full_unstemmed | High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia |
| title_short | High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia |
| title_sort | high quality genome assembly of olea europaea subsp cuspidata provides insights into its resistance to fungal diseases in the summer rain belt in east asia |
| topic | genome assembly Olea europaea susceptibility gene demographic history nature selection |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.879822/full |
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