Tambong James T
Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.
PLoS One. 2017 Mar 20;12(3):e0172295. doi: 10.1371/journal.pone.0172295. eCollection 2017.
Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.
密执安棒形杆菌亚种是重要的植物细菌病原体，可在多种农作物中引发毁灭性病害。人们对这些病原体的基因组结构了解甚少。在此，对5个亚种（密执安棒形杆菌密歇根亚种，Cmi；密执安棒形杆菌马铃薯环腐亚种，Cms；密执安棒形杆菌内布拉斯加亚种，Cmn；密执安棒形杆菌隐匿亚种，Cmi；以及密执安棒形杆菌辣椒亚种，Cmc）的完整基因组进行了分析。本研究基于16S rRNA和基于基因组的DNA同源性评估了这些亚种的分类地位，并得出结论：有充分证据可将部分亚种提升至种级水平。比较基因组学分析表明，在DNA结构图谱和注释特征上存在明显不同的基因组特征。基于直系同源基因分析，所有亚种共有的编码序列（CDS）约有2300个；Cms具有的亚种特异性CDS数量最多，其中大部分是移动元件，这表明Cms可能更容易发生外源基因的易位。Cms和Cmi的假基因数量最多，这表明其基因组可能存在潜在的退化现象。概述了可能参与冷/热休克、解毒、氧化应激、渗透调节和碳利用的应激反应因子。例如，编码胞外多糖II的wco基因簇高度保守，而催化蔗糖-6-磷酸水解生成葡萄糖-6-磷酸和果糖的蔗糖-6-磷酸水解酶则高度分化。该酶的一种独特的第二种形式仅存在于Cmn NCPPB 2581中。此外，在其他亚种中发现的28个质粒携带的CDS在已知不携带质粒的Cmn染色体基因组中具有同源物。这些CDS包括与致病相关的因子，如内切纤维素酶E1和β-葡萄糖苷酶。本文给出的结果为密执安棒形杆菌5个核心亚种的基因组功能组织提供了见解，有助于更好地了解这些植物细菌。
