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Journal of Integrative Agriculture  2020, Vol. 19 Issue (4): 906-920    DOI: 10.1016/S2095-3119(19)62883-2
Special Focus: Bleeding canker of pear-An emerging devastating disease Advanced Online Publication | Current Issue | Archive | Adv Search |
Genomic characteristics of Dickeya fangzhongdai isolates from pear and the function of type IV pili in the chromosome
CHEN Bin1, TIAN Yan-li1, ZHAO Yu-qiang2, WANG Yuan-jie1, CHUAN Jia-cheng3, LI Xiang3, HU Bai-shi
1 College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, P.R.China
2 Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen)/Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, P.R.China
3 Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, PE C1A5T1, Canada
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Dickeya fangzhongdai, the causal agent of bleeding canker of pear, is a new member of the Dickeya genus and the only one that infects woody plants.  Recent studies have reclassified several Dickeya isolates as D. fangzhongdai, which were isolated from various environments, including water, Phalaenopsis sp. and Aglaonema sp.  To provide genomic characterization of D. fangzhongdai isolates from pear, the genomes of D. fangzhongdai strain JS5 (=China General Microbiological Culture Collection Center, CGMCC 1.15464T=DSM 101947T), along with two other isolates, LN1 and QZH3, were sequenced and compared to those of other Dickeya spp.  Homology greater than 99% was observed among three D. fangzhongdai strains.  Plasmid, type IV secretion system (T4SS) and type IV pili (TFPs) were found in genomes of D. fangzhongdai isolates.  Comparative analysis of the type III secretion systems (T3SS), type III secretion effectors (T3SE), plant cell wall degradation enzymes (PCWDE) and membrane transport proteins of Dickeya spp. showed some differences which might reflect the variations of virulence, phylogenetic and phenotypic characteristics of Dickeya spp.  In addition, deletion mutant of TFP in D. fangzhongdai JS5 showed no twitching motility and reduced virulence and biofilm formation.  The fingdings of the distinctive plasmid, T4SS and TFPs, as well as the differences of T3SE, PCWDE and membrane transport proteins make D. fangzhongdai isolates unique.  These results also suggested that acquisition of virulence genes by horizontal gene transfer might play some role in the genetic variation of D. fangzhongdai.
Keywords:  Dickeya fangzhongdai        comparative genomics        virulence        type IV pili  
Received: 13 November 2019   Accepted:
Fund: This research was supported by the 111 International Cooperation Grant 2.0 (BP0719029) to Nanjing Agricultural University, China, from the Chinese government and Canadian Interdepartmental funding of Genomics Research and Development Initiatives (GRDI).
Corresponding Authors:  Correspondence HU Bai-shi, E-mail:; LI Xiang, E-mail:    
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CHEN Bin, TIAN Yan-li, ZHAO Yu-qiang, WANG Yuan-jie, CHUAN Jia-cheng, LI Xiang, HU Bai-shi. 2020. Genomic characteristics of Dickeya fangzhongdai isolates from pear and the function of type IV pili in the chromosome. Journal of Integrative Agriculture, 19(4): 906-920.

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