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<p>This study employed a genome-based approach, utilizing digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and phylogenomic analyses to re-evaluate species relationships within <i>Deinococcus</i> members. Three clusters of closely related species emerged: (i) <i>D. ficus</i> and <i>D. enclensis</i> showed high genomic similarity (dDDH 79.5%, ANI 97.2%, AAI 97.6%), despite low 16S rRNA identity (97.6%), indicating they are conspecific; (ii) <i>D. seoulensis</i> and <i>D. knuensis</i> exhibited genomic coherence (dDDH 77.8%, ANI 97.6%, AAI 97.6%) with sufficient divergence for subspecies designation; and (iii) <i>D. arenae</i>, <i>D. kurensis</i>, and <i>D. actinosclerus</i> revealed that <i>D. arenaae</i> and <i>D. kurensis</i> belong to the same genomospecies (dDDH 81.0%, ANI 97.9%, AAI 98.0%), while <i>D. actinosclerus</i> remained distinct (dDDH 64.5–64.7%, ANI 96.2–96.4%). Therefore, we propose <i>D. enclensis</i> as a later heterotypic synonym of <i>D. ficus</i>; <i>D. knuensis</i> as a later heterotypic synonym of <i>D. seoulensi</i>, with the designation of <i>D. seoulensis</i> subsp. <i>seoulensis</i> subsp. nov. and <i>D. seoulensis</i> subsp. <i>knuensis</i> subsp. nov.; and <i>D. kurensis</i> as a later heterotypic synonym of <i>D. arenae</i>. These revisions underscore the superiority of genomic methods over traditional approaches, offering a robust taxonomic framework for <i>Deinococcus</i>.</p>

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Comprehensive phylogenomic analyses support the reclassification of several species belonging to the Deinococcus genus

  • 期刊论文

  • 发表日期：

    2026年5月13日

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  • Khaoula Bouznada,
  • Rafika Saker,
  • Hadj Ahmed Belaouni,
  • Atika Meklat

摘要

This study employed a genome-based approach, utilizing digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and phylogenomic analyses to re-evaluate species relationships within Deinococcus members. Three clusters of closely related species emerged: (i) D. ficus and D. enclensis showed high genomic similarity (dDDH 79.5%, ANI 97.2%, AAI 97.6%), despite low 16S rRNA identity (97.6%), indicating they are conspecific; (ii) D. seoulensis and D. knuensis exhibited genomic coherence (dDDH 77.8%, ANI 97.6%, AAI 97.6%) with sufficient divergence for subspecies designation; and (iii) D. arenae, D. kurensis, and D. actinosclerus revealed that D. arenaae and D. kurensis belong to the same genomospecies (dDDH 81.0%, ANI 97.9%, AAI 98.0%), while D. actinosclerus remained distinct (dDDH 64.5–64.7%, ANI 96.2–96.4%). Therefore, we propose D. enclensis as a later heterotypic synonym of D. ficus; D. knuensis as a later heterotypic synonym of D. seoulensi, with the designation of D. seoulensis subsp. seoulensis subsp. nov. and D. seoulensis subsp. knuensis subsp. nov.; and D. kurensis as a later heterotypic synonym of D. arenae. These revisions underscore the superiority of genomic methods over traditional approaches, offering a robust taxonomic framework for Deinococcus.