Dobhal Shefali, Hugouvieux-Cotte-Pattat Nicole, Arizala Dario, Sari Gamze Boluk, Chuang Shu-Cheng, Alvarez Anne M, Arif Mohammad
Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.
Univ Lyon, CNRS, INSA Lyon, UCBL, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France.
bioRxiv. 2024 Oct 30:2024.10.29.620964. doi: 10.1101/2024.10.29.620964.
Recently, species clustering within has been identified as complex, encompassing validly published names, including and , with some strains potentially delineating new species. In this study, genomes of strains isolated from a bacterial heart rot outbreak in pineapple ( var. ) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93-99.9% and 91.8-99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of and ranged from 94.4-95.9% and 57.2-66.5%, respectively. These values fall below the proposed boundaries for new species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, , multi-locus sequence analysis (MLSA) of 10 housekeeping genes, whole-genome, and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the complex, with as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the spp. nitrogenase gene cluster, was found in the genome of the seven pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological, and phylogenomic analyses, we propose the reclassification in a new species of the five pineapple strains from Hawaii A5391, A5410, A5611, A6136, and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as . We propose the name sp. nov. for this taxon, represented by the type strain A5410 (= ICMP 25020 = LMG 33197).
最近,已确定[具体属名]内的物种聚类情况很复杂,包含有效发表的名称,如[具体名称1]和[具体名称2],一些菌株可能会划分出新物种。在本研究中,对从夏威夷瓦胡岛菠萝(品种[具体品种名])细菌性心腐病爆发中分离出的菌株基因组,以及来自马来西亚菠萝的两个菌株进行了测序。测序基因组之间的直系同源平均核苷酸同一性(ANI)和数字DNA - DNA杂交(dDDH)值分别在98.93 - 99.9%和91.8 - 99.9%之间,支持将七个菌株归为同一物种。这七个菌株与[相关属名1]和[相关属名2]的模式菌株之间的ANI和dDDH值比较分别在94.4 - 95.9%和57.2 - 66.5%之间。这些值低于新物种命名提议的界限,支持划分出一个新物种。系统发育分析,包括16S rRNA、[具体基因名]、10个管家基因的多位点序列分析(MLSA)、全基因组和泛基因组分析,结果一致,并揭示出一个独特的单系分支,将这些菌株与[具体属名]复合体的其他成员区分开来,[具体物种名]是其最亲近的亲缘物种。值得注意的是,在这七个菠萝菌株的基因组中发现了一个由28个基因组成的固氮基因簇,类似于[相关物种名]的固氮酶基因簇。基于多相方法,包括ANI、dDDH、生化、生理和系统基因组分析,我们提议将来自夏威夷的五个菠萝菌株A5391、A5410、A5611、A6136和A6137,以及来自马来西亚的两个菠萝菌株CFBP 1272和CFBP 1278(之前被归类为[具体名称])重新分类为一个新物种。我们提议将这个分类单元命名为[新物种名] sp. nov.,模式菌株为A5410(= ICMP 25020 = LMG 33197)。