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https://doi.org/10.1186/s12864-015-1545-x
Title: | The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species | Authors: | Zhou, J Cheng, Y Lv, M Liao, L Chen, Y Gu, Y Liu, S Jiang, Z Xiong, Y Zhang, L |
Keywords: | bacterial DNA fatty acid unclassified drug virulence factor zeamine macrolide polyamine zeamine Article bacterial chromosome bacterial flagellum bacterial gene bacterial strain bacterial virulence bacterium isolation controlled study Dickeya Dickeya chrysanthemi Dickeya paradisiaca Dickeya zeae fatty acid metabolism fli gene gene cluster gene rearrangement gene sequence genetic code genetic variability nonhuman nucleotide sequence Pantoea Pantoea ananatis rice sequence homology species difference strain difference zms gene bacterial genome chromosomal mapping Enterobacteriaceae genetics genomics metabolism microbiology Oryza pathogenicity phylogeny plant disease Bacteria (microorganisms) Dickeya Dickeya paradisiaca Dickeya zeae Dicotyledoneae Liliopsida Pantoea ananatis Base Sequence Chromosome Mapping Enterobacteriaceae Genome, Bacterial Genomics Macrolides Oryza Phylogeny Plant Diseases Polyamines |
Issue Date: | 2015 | Citation: | Zhou, J, Cheng, Y, Lv, M, Liao, L, Chen, Y, Gu, Y, Liu, S, Jiang, Z, Xiong, Y, Zhang, L (2015). The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species. BMC Genomics 16 (1) : 571. ScholarBank@NUS Repository. https://doi.org/10.1186/s12864-015-1545-x | Rights: | Attribution 4.0 International | Abstract: | 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. Conlusion: 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. © 2015 Zhou et al. | Source Title: | BMC Genomics | URI: | https://scholarbank.nus.edu.sg/handle/10635/181439 | ISSN: | 14712164 | DOI: | 10.1186/s12864-015-1545-x | Rights: | Attribution 4.0 International |
Appears in Collections: | Elements Staff Publications |
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