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Related Experiment Video

Updated: May 8, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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Phylogeny and classification of Dickeya based on multilocus sequence analysis.

Glorimar Marrero1, Kevin L Schneider1, Daniel M Jenkins1

  • 1Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.

International Journal of Systematic and Evolutionary Microbiology
|September 5, 2013
PubMed
Summary

Bacterial heart rot in pineapple was caused by Dickeya bacteria. Multilocus sequence analysis and genomic data suggest reclassifying several Dickeya strains, improving bacterial taxonomy and disease management.

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Area of Science:

  • Bacteriology
  • Plant Pathology
  • Genomics

Background:

  • Pineapple bacterial heart rot outbreaks in Hawaii (2003, 2006) were linked to an unidentified Dickeya species.
  • Accurate bacterial species identification is crucial for understanding disease epidemiology and implementing control measures.

Purpose of the Study:

  • To classify Dickeya strains from pineapple and determine their phylogenetic relationships.
  • To evaluate multilocus sequence analysis (MLSA) markers for Dickeya species resolution.
  • To re-evaluate the taxonomic status of specific Dickeya strains using genomic data.

Main Methods:

  • Multilocus sequence analysis (MLSA) using partial gene sequences (dnaA, dnaJ, dnaX, gyrB, recN).
  • Phylogenetic analysis of individual and concatenated gene sequences.
  • Average Nucleotide Identity (ANI) and tetranucleotide frequency analysis of sequenced genomes.

Main Results:

  • Pineapple-associated Dickeya strains formed a distinct clade closely related to Dickeya zeae but did not meet genomic thresholds for this species.
  • The recN marker showed the highest resolution for Dickeya species identification within the MLSA.
  • Genomic analyses (ANI) supported reclassifying D. dadantii Ech586 and D. dadantii Ech703 to Dickeya zeae and Dickeya paradisiaca, respectively, and D. zeae Ech1591 to Dickeya chrysanthemi.

Conclusions:

  • The study refines the taxonomy of Dickeya species associated with pineapple bacterial heart rot.
  • MLSA, particularly using the recN marker, is effective for Dickeya phylogenetic studies.
  • Genomic reclassifications provide a more accurate understanding of Dickeya diversity and host associations.