Data_Sheet_1_Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants.PDF

Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763T, CPCC 203386T, CPCC 205716T, CPCC 203406T, 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 203406T and CPCC 203407 being classified in the same species. For which the names Herbiconiux aconitum sp. nov. (type strain CPCC 205763T = I19A-01430T = CGMCC 1.60067T), Herbiconiux daphne sp. nov. (type strain CPCC 203386T = I10A-01569T = DSM 24546T = KCTC 19839T), Herbiconiux gentiana sp. nov. (type strain CPCC 205716T = I21A-01427T = CGMCC 1.60064T), and Herbiconiux oxytropis sp. nov. (type strain CPCC 203406T = I10A-02268T = DSM 24549T = KCTC 19840T) 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.

五株革兰氏染色阳性、需氧、非游动性放线菌菌株，分别命名为CPCC 205763T、CPCC 203386T、CPCC 205716T、CPCC 203406T和CPCC 203407，源自与中国四种传统药用植物相关的不同生态系统。这些菌株的16S rRNA基因序列与微杆菌科Herbiconiux属的成员密切相关，与Herbiconiux属的四个有效命名的物种相似度高达97.4%-99.7%。基于16S rRNA基因序列和核心基因组的系统发育树表明，这些菌株聚集在微杆菌科Herbiconiux属的谱系中。整体基因组相关性指数（ANI和dDDH值）以及菌株的表型特性（形态学、生理学和化学分类学特征）均有力地支持将其归入Herbiconiux属，代表四个新物种，其中菌株CPCC 203406T和CPCC 203407被归类为同一物种。因此，分别提出了Herbiconiux aconitum sp. nov.（模式菌株CPCC 205763T = I19A-01430T = CGMCC 1.60067T）、Herbiconiux daphne sp. nov.（模式菌株CPCC 203386T = I10A-01569T = DSM 24546T = KCTC 19839T）、Herbiconiux gentiana sp. nov.（模式菌株CPCC 205716T = I21A-01427T = CGMCC 1.60064T）和Herbiconiux oxytropis sp. nov.（模式菌株CPCC 203406T = I10A-02268T = DSM 24549T = KCTC 19840T）的名称。在这五个菌株的基因组中，检索到了可能编码酰胺酶、内切葡聚糖酶、磷酸酶和超氧化物歧化酶的基因，这些基因被归类为与植物生长促进（PGP）功能相关的生物合成基因/基因簇。IAA产生、纤维素降解和抗氧化实验的阳性结果进一步证实了它们的PGP生物功能的潜力。Herbiconiux属的全基因组分析支持了多相分类学结果，并确认了它们的生物功能潜力。