Complete Genome Sequence of Dickeya oryzae Strain A5272 Isolated During Pineapple Heart Rot Outbreak in Hawaii
Year: 2025
Type: article
Abstract: The complete genome of Dickeya oryzae strain A5272, isolated from a 2004 pineapple heart rot outbreak in Hawaii, was sequenced using PacBio RSII. The strain was linked to the pineapple propagative material imported from Costa Rica and Honduras. The genome assembly revealed a size of 4.69 Mbp, with a G + C content of 53.5%, and contains 4,193 putative coding genes, 22 rRNAs, and 75 tRNAs. The assembly was of high quality, yielding a single contig with 98.2% completeness and 0.3% contamination. Comparative genomic analysis using digital DNA–DNA hybridization and OrthoANIu metrics revealed that the strain is closely related to the Dickeya zeae complex. A total of 42 genomic islands were identified, several of which are associated with virulence and antibiotic resistance. The genome encodes key virulence factors such as plant cell wall-degrading enzymes, including cellulases, pectate lyases, and xylose metabolism genes, as well as proteins involved in pilus assembly, transport, and secretion mechanisms. Interestingly, the genome does not appear to encode a type III secretion system and lacks the nitrogen fixation nif cluster found in some other plant-pathogenic Dickeya strains. Additionally, only one gene of the zeamine biosynthesis cluster, involved in antimicrobial activity, was identified in the genome of Dickeya oryzae A5272. This sequence provides valuable insights into the genomic characteristics of Dickeya oryzae and its potential impact on crop health. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Source: PhytoFrontiers™
Authors: Komal, Shefali Dobhal, Dario Arizala, Gamze Boluk, Anne M. Alvarez, Mohammad Arif
Institutions: University of Hawaiʻi at Mānoa, University of Hawaii System
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: diamond
OpenAlex ID: W4409106722