Members of Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g. alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter spp. strains occupy a great portion of genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) causing bacterial canker disease considered one of the destructive seed-borne agents of the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory consequences in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter spp. strains - including the type strains of newly described subspecies - to provide a precise insight into the diversity of tomato-associated members of the genus, and further clarify taxonomic status of the strains using genotypic and phenotypic features. Results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e. C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the non-pathogenic strains, a number of pathogenicity related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results advocate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter spp. strains to facilitate differentiation of the lineages in quarantine inspections.

Importance Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant pathogenic members of the genus (e.g. C. michiganensis sensu stricto and C. sepedonicus infecting tomato and potato plants, respectively) are included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. occupy a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and subjected to the quarantine inspections. Hence, discrimination of the pathogenic and non-pathogenic Clavibacter spp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost efficiently management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview on the phylogenetic and genomic differences between the pathogenic and non-pathogenic tomato-associated Clavibacter spp. strains. We have also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e. C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli) should be reconsidered.

棒状杆菌属的成员。是在经济上重要的细菌性植物病原体，可感染多种多样的农作物（例如苜蓿，玉米，马铃薯，番茄和小麦）。番茄相关的棒杆菌属。菌株占据属的遗传多样性的大部分，和C.密执安狭义（原C.密执安亚种密执安）引起细菌性溃疡病，被认为是全世界农作物的破坏性种子传播媒介之一。但是，该属的当前分类学描述并未反映菌株的现有多样性，从而导致对病原体的检疫调查结果不理想。在这项研究中，我们使用了棒杆菌属的所有可用基因组序列。菌株-包括新近描述的亚种的菌株-提供对番茄相关属的多样性的精确了解，并利用基因型和表型特征进一步阐明菌株的分类学地位。系统发育分析的结果表明，在所研究的菌株中存在9个假设的新物种。三个新亚种（即密歇根梭菌）都没有亚种 加利福尼亚州密歇根州C. subsp。chilensis和密歇根C.subsp。菜豆）包括在番茄致病的密歇根州立严格的谱系中。尽管比较基因组学揭示了在非致病性菌株中缺乏chp和tomA致病性决定基因簇，但是所有菌株中都存在许多与致病性相关的基因，无论其致病性如何。总而言之，我们的研究结果表明需要对番茄相关的细杆菌进行正式的分类学重新考虑。spp。有助于在检疫检查中区分血统的菌株。

重要性 棒杆菌属。是在经济上重要的细菌植物病原体，可感染一系列不同的农作物，例如苜蓿，玉米，胡椒，马铃薯，番茄和小麦。一些属的植物病原成员（如 C.密执安狭义和C. sepedonicus感染番茄和马铃薯植株，分别）都包括在欧洲和地中海植物保护组织检疫病原体A2（高风险）名单（ EPPO）。尽管番茄与杆状杆菌属有关。占据了该属中遗传多样性的很大一部分，仅属于密歇根梭菌的菌株（以前称为密歇根梭菌）亚种 密歇根州（Michiganensis）引起番茄的细菌性溃疡病并接受检疫检查。因此，可以区分致病性和非致病性棒杆菌属。与番茄种子和移植物有关的菌株在准确检测和经济有效地控制该疾病方面起着关键作用。另一方面，有关属的不同谱系的遗传含量的详细信息将导致基因组信息特异性检测技术的发展。在这项研究中，我们概述了致病性和非致病性番茄相关的棒杆菌属之间的系统发育和基因组差异。株。我们还注意到，新引入的亚种的分类学地位C.密执安（即C.密执安亚种californiensis，C.密执安亚种chilensis的和C.密执安亚种菜豆）应该被重新考虑。