Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
Int J Syst Evol Microbiol. 2024 Sep;74(9). doi: 10.1099/ijsem.0.006523.
The pathovar-based taxonomy of the group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the complex. This polyphasic approach taxonomically assigned the 11 pathovars of complex into three distinct species, two of which are new: , sp. nov. and sp. nov. consists of three pathovars: pv. (=pv. ), pv. strain A ICMP 16316 and pv. (=pv. ). sp. nov. encompasses the pv. strain LMG 679 and pv. strain B ICMP 16317 with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, sp. nov., consists of the remaining five designated pathovars (pv. , pv. pv. , pv. and pv. ) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. and showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of sp. nov. exhibited 20% less C iso and 40% more C iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, sp. nov. and sp. nov. with type strains LMG 679 (=NCPPB 1944) and LMG 726 (=NCPPB 2700), respectively.
由于植物宿主范围和宿主特异性水平的重叠，基于路径变种的 组分类非常混乱。在这里，我们使用全基因组序列参数（数字 DNA-DNA 杂交和基于blast 的平均核苷酸同一性）、系统基因组学、生物化学和表型数据对 复合体的 11 个已知路径变种进行了分类分析。这种多相方法将 复合体的 11 个路径变种分为三个不同的种，其中两个是新种： ， sp. nov. 和 sp. nov. 由三个路径变种组成：pv. （=pv. ）、pv. 菌株 A ICMP 16316 和 pv. （=pv. ）。 sp. nov. 包含 pv. 菌株 LMG 679 和 pv. 菌株 B ICMP 16317，基因组相似度为 92.7%（dDDH）和 99.0%（ANIb），提示分类相似的基因型。另一个新种 sp. nov. 由其余五个指定的路径变种（pv. 、pv. 、pv. 、pv. 和 pv. ）组成，其 dDDH 和 ANIb 值变化很大，范围分别为 74.5% 至 93.0%和 96.7% 至 99.2%，表明这是一个非常分化的分类群。只有 pv. 和 pv. 菌株显示出最高的基因组相似度，分别为 93.0%（dDDH）和 99.2%（ANIb），表明这两个路径变种是同义词，因为它们感染相同的植物宿主。dDDH 和 ANI 数据得到了系统基因组学聚类的支持。脂肪酸含量相似，但 sp. nov. 的模式菌株比其他物种少 20%的 Ciso 和多 40%的 Ciso 脂肪酸。基于表型、生物化学和全基因组序列数据，我们提出了两个新种，即 sp. nov. 和 sp. nov. ，其模式菌株分别为 LMG 679（=NCPPB 1944）和 LMG 726（=NCPPB 2700）。
