School of Food and Agriculture, University of Maine, Orono, ME 04469.
School of Biology and Ecology, University of Maine, Orono, ME 04469.
Plant Dis. 2021 Dec;105(12):3946-3955. doi: 10.1094/PDIS-03-21-0587-RE. Epub 2021 Nov 30.
has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.
自 2015 年以来，这种病原体已导致美国东部地区黑胫病和软腐病的爆发。为了研究病原体的遗传多样性，对来自美国疫情的 16 株菌株的基因组进行了比较分析。对来自美国疫情的 16 株菌株的全基因组进行了组装，并与从马铃薯或康乃馨中分离出的 16 株先前测序的 菌株的基因组进行了比较。在这 32 株菌株中，根据系统发育分析区分出了 8 个不同的进化枝。疫情菌株分为 3 个进化枝，其中大多数菌株属于进化枝 I。进化枝 I 菌株是独特且同质的，表明该菌株最近从替代宿主或环境来源入侵了马铃薯生产。32 株菌株的泛基因组包含 6693 个基因，其中 3377 个是核心基因。通过筛选来自所有美国菌株的与毒力相关的主要蛋白亚基，我们发现许多与毒力相关的基因簇，如植物细胞壁降解酶基因、鞭毛和趋化性相关基因、双组分调控基因和 I/II/III 型分泌系统基因高度保守，但 IV 型和 VI 型分泌系统基因存在差异。进化枝 I 菌株编码两个 IV 型分泌系统簇，而进化枝 II 和 III 菌株只编码一个簇。进化枝 I 和 II 菌株编码的 VgrG/PAAR 刺突蛋白比进化枝 III 菌株多一个。因此，我们预测，额外的与毒力相关基因的存在可能使独特的进化枝 I 菌株在美国疫情中占主导地位。
