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Journal of Integrative Agriculture  2018, Vol. 17 Issue (04): 878-891    DOI: 10.1016/S2095-3119(17)61867-7
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Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity
QIAN Kun1*, LI Deng-hui1*, LIN Run-mao1, 2, SHI Qian-qian1, MAO Zhen-chuan1, YANG Yu-hong1, FENG Dong-xin1, XIE Bing-yan1, 3 
1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2 College of Life Sciences, Beijing Normal University, Beijing 100875, P.R.China
3 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, P.R.China
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Abstract  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.
Keywords:  Phytophthora        carbohydrate esterase gene prediction        comparative genomic analysis        evolution        diversity  
Received: 07 July 2017   Accepted:

This work was supported by the Special Fund for Agro-scientific Research in the Public Interest, China (201303018), the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS) and the emarked fund for the China Agriculture Research System (CARS-25-B-01).

Corresponding Authors:  Correspondence FENG Dong-xin, Tel: +86-10-82109545, Fax: +86-10-62174123, E-mail:; XIE Bing-yan, Tel: +86-10-82109545, Fax: +86-10-62174123, E-mail:   
About author:  QIAN Kun, E-mail:; * These authors contributed equally to this study.

Cite this article: 

QIAN Kun, LI Deng-hui, LIN Run-mao , SHI Qian-qian, MAO Zhen-chuan, YANG Yu-hong, FENG Dong-xin, XIE Bing-yan . 2018. Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity. Journal of Integrative Agriculture, 17(04): 878-891.

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