Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants

Yang Deng; Zhu-Ming Jiang; Xue-Fei Han; Jing Su; Li-Yan Yu; Wei-Hong Liu; Yu-Qin Zhang

doi:10.3389/fmicb.2023.1119226

Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants

Front Microbiol. 2023 Feb 28:14:1119226. doi: 10.3389/fmicb.2023.1119226. eCollection 2023.

Authors

Yang Deng^{1

2}, Zhu-Ming Jiang^{1

2}, Xue-Fei Han^{1

2}, Jing Su¹, Li-Yan Yu¹, Wei-Hong Liu³, Yu-Qin Zhang^{1

2}

Affiliations

¹ Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
² State Key Laboratory of Dao-di Herb, Beijing, China.
³ Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China.

Abstract

Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763^T, CPCC 203386^T, CPCC 205716^T, CPCC 203406^T, and CPCC 203407 were obtained from different ecosystems associated with four kinds of Chinese traditional medicinal plants. The 16S rRNA gene sequences of these five strains showed closely related to members of the genus Herbiconiux of the family Microbacteriaceae, with the highest similarities of 97.4-99.7% to the four validly named species of Herbiconiux. In the phylogenetic trees based on 16S rRNA gene sequences and the core genome, these isolates clustered into the clade of the genus Herbiconiux within the lineage of the family Microbacteriaceae. The overall genome relatedness indexes (values of ANI and dDDH) and the phenotypic properties (morphological, physiological and chemotaxonomic characteristics) of these isolates, readily supported to affiliate them to the genus Herbiconiux, representing four novel species, with the isolates CPCC 203406^T and CPCC 203407 being classified in the same species. For which the names Herbiconiux aconitum sp. nov. (type strain CPCC 205763^T = I19A-01430^T = CGMCC 1.60067^T), Herbiconiux daphne sp. nov. (type strain CPCC 203386^T = I10A-01569^T = DSM 24546^T = KCTC 19839^T), Herbiconiux gentiana sp. nov. (type strain CPCC 205716^T = I21A-01427^T = CGMCC 1.60064^T), and Herbiconiux oxytropis sp. nov. (type strain CPCC 203406^T = I10A-02268^T = DSM 24549^T = KCTC 19840^T) were proposed, respectively. In the genomes of these five strains, the putative encoding genes for amidase, endoglucanase, phosphatase, and superoxidative dismutase were retrieved, which were classified as biosynthetic genes/gene-clusters regarding plant growth-promotion (PGP) functions. The positive results from IAA-producing, cellulose-degrading and anti-oxidation experiments further approved their potential PGP bio-functions. Pangenome analysis of the genus Herbiconiux supported the polyphasic taxonomy results and confirmed their bio-function potential.

Keywords: Herbiconiux; medicinal plants; pangenome; plant growth-promotion; polyphasic taxonomy.