The consolidated and reconciled annotations from all of the WGS strains used in this study

Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of Pagg to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

Methods
Eighty-one genomes assembled as part of this study were combined with 100 high-quality genome assemblies from NCBI Genbank (Table S3). Genomes were re-annotated with Prokka [@Seemann2014] for pangenome analysis with Roary [@Page2015] to identify core and accessory genes. Custom scripts were used to reconcile the CDS records of the Prokka, Genbank, and RefSeq annotations for each genome. For the process, CDS records were considered to be synonymous, if the coordinates for their stop codon were equal. If the coordinates of the start codon of synonymous CDS records were not equal, the records were marked as "interesting".

成团泛菌(Pantoea agglomerans)是美国已报道的4种可引发洋葱球茎细菌性腐烂的泛菌属(Pantoea)物种之一。然而，并非所有成团泛菌菌株均对洋葱具有致病性。本研究对与洋葱相关的成团泛菌菌株进行了表征，以阐明洋葱致病型成团泛菌的遗传与基因组特征。我们从公共菌种保藏中心、研究实验室以及美国11个州历时多年的调查中，收集了超过300株与表现症状的洋葱植株及球茎相关的成团泛菌菌株。将本研究获得的87个基因组组装序列与100条高质量的公共成团泛菌基因组组装序列相结合，我们鉴定出两个支持度良好的成团泛菌系统发育群(phylogroup)。仅在系统发育群II中发现了可对洋葱造成严重症状的菌株，这些菌株均编码HiVir pantaphos生物合成基因簇，证实了HiVir作为致病性因子的作用。成团泛菌的HiVir基因簇存在于两种不同的质粒环境中：1) 在保守型成团泛菌质粒(pAggl)上作为附属基因簇存在；2) 在洋葱菌株中普遍存在的镶嵌型质粒(pOnion)上。对闭合基因组的分析显示，pOnion质粒携带可赋予对葱属植物硫代亚磺酸酯类防御性化学物质耐受性的alt基因，且多数质粒携带可赋予铜抗性的cop基因。本研究证实，pOnion质粒pCB1C可作为一种天然可迁移的致病性质粒，能够将成团泛菌系统发育群I的菌株（包括环境菌株）转化为洋葱的强致病菌株。本研究表明，质粒及质粒生态在介导成团泛菌与洋葱植株的互作中发挥核心作用，这对洋葱细菌性病害的防控具有潜在应用价值。

方法
本研究组装得到的81个基因组序列，与来自NCBI基因库(NCBI Genbank)的100条高质量基因组组装序列相结合（补充表S3）。使用Prokka[@Seemann2014]对所有基因组进行重新注释，以结合Roary[@Page2015]开展泛基因组(pangenome)分析，从而鉴定核心基因与附属基因。采用自定义脚本对每个基因组的Prokka、Genbank及RefSeq注释的编码序列(CDS, Coding Sequence)记录进行整合校正。在此流程中，若两条CDS记录的终止密码子坐标完全一致，则判定为同义CDS；若同义CDS的起始密码子坐标存在差异，则将此类记录标记为“值得关注”。