Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity
A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase (CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and ev...
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| Format: | Article |
| Language: | English |
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Elsevier
2018-04-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311917618677 |
| _version_ | 1831539086276427776 |
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| author | Kun QIAN Deng-hui LI Run-mao LIN Qian-qian SHI Zhen-chuan MAO Yu-hong YANG Dong-xin FENG Bing-yan XIE |
| author_facet | Kun QIAN Deng-hui LI Run-mao LIN Qian-qian SHI Zhen-chuan MAO Yu-hong YANG Dong-xin FENG Bing-yan XIE |
| author_sort | Kun QIAN |
| collection | DOAJ |
| description | A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase (CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs. |
| first_indexed | 2024-12-16T23:35:20Z |
| format | Article |
| id | doaj.art-0550584fc5424452b59e9cdd49376752 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-16T23:35:20Z |
| publishDate | 2018-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-0550584fc5424452b59e9cdd493767522022-12-21T22:11:46ZengElsevierJournal of Integrative Agriculture2095-31192018-04-01174878891Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversityKun QIAN0Deng-hui LI1Run-mao LIN2Qian-qian SHI3Zhen-chuan MAO4Yu-hong YANG5Dong-xin FENG6Bing-yan XIE7Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; Correspondence FENG Dong-xin, Tel: +86-10-82109545, Fax: +86-10-62174123Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, P.R. China; XIE Bing-yan, Tel: +86-10-82109545, Fax: +86-10-62174123A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase (CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.http://www.sciencedirect.com/science/article/pii/S2095311917618677Phytophthoracarbohydrate esterase gene predictioncomparative genomic analysisevolution, diversity |
| spellingShingle | Kun QIAN Deng-hui LI Run-mao LIN Qian-qian SHI Zhen-chuan MAO Yu-hong YANG Dong-xin FENG Bing-yan XIE Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity Journal of Integrative Agriculture Phytophthora carbohydrate esterase gene prediction comparative genomic analysis evolution, diversity |
| title | Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity |
| title_full | Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity |
| title_fullStr | Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity |
| title_full_unstemmed | Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity |
| title_short | Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity |
| title_sort | rediscovery and analysis of phytophthora carbohydrate esterase ce genes revealing their evolutionary diversity |
| topic | Phytophthora carbohydrate esterase gene prediction comparative genomic analysis evolution, diversity |
| url | http://www.sciencedirect.com/science/article/pii/S2095311917618677 |
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