title: The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species.
abstract: BACKGROUND
  Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known.
  
  
  RESULTS
  The complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis.
  
  
  CONCLUSIONS
  Our findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution.
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. jianuanzhou@scau.edu.cn.
authors.forename: Jianuan
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. jinlingmeng@163.com.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. mingfalv2010@163.com.
authors.forename: Mingfa
authors.initials: M
authors.lastname: Lv
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. lishengliao@outlook.com.
authors.forename: Lisheng
authors.initials: L
authors.lastname: Liao
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. chenyufanscau@gmail.com.
authors.forename: Yufan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. yfgu12@163.com.
authors.forename: Yanfang
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. l.liu19@hotmail.com.
authors.forename: Shiyin
authors.initials: S
authors.lastname: Liu
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. zdjiang@scau.edu.cn.
authors.forename: Zide
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: State Key laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China. mody0911@gmail.com.
authors.forename: Yuanyan
authors.initials: Y
authors.lastname: Xiong
authors.affiliation: Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. lhzhang01@scau.edu.cn.|Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore. lhzhang01@scau.edu.cn.
authors.forename: Lianhui
authors.initials: L
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D004755:Enterobacteriaceae / Q000235:genetics* / Q000472:pathogenicity; D016680:Genome, Bacterial; D023281:Genomics; D018942:Macrolides / Q000378:metabolism; D012275:Oryza / Q000235:genetics / Q000382:microbiology; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D011073:Polyamines / Q000378:metabolism
chemical_list: D018942:Macrolides; D011073:Polyamines; C547236:zeamine