1 Department of Animal Behaviour & Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
2 Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
OMICS. 2019 Apr;23(4):224-236. doi: 10.1089/omi.2019.0005.
is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen, causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of or the host-specific strains' pan-genomes. We report on livestock-associated (LA-) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA-' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA- genomes. We call for comparative microbial and pan-genome research between human and LA that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.
不仅是正常菌群的一部分，还是与微生物基因组学、公共卫生和兽医医学相关的机会性病原体。除了是一种众所周知的人类病原体外，还会引起奶牛、绵羊、山羊和猪等重要经济家畜的各种感染。很少有研究检查过 或宿主特异性菌株的泛基因组。我们报告了与家畜相关的（LA-）泛基因组，并表明毒力不是其基因组进化的主要关注点。从 NCBI 中检索到了 LA- 的完整基因组，并通过高速 Roary 管道构建了泛基因组。泛基因组大小为 4637 个簇，而 42.46%的泛基因组与核心基因组相关。我们发现 1268 个基因与菌株独特的基因组相关，其余 1432 个簇与辅助基因组相关。核心基因的 COG（同源群簇的蛋白质）分析显示，34%的簇与负责氨基酸和无机离子转运的代谢有关（COG 类别 E 和 P），其次是碳水化合物代谢（类别 G）。毒力基因分析显示，核心基因负责抗吞噬作用和铁摄取。泛基因组的流动性计算为 0.082±0.025。重要的是，阳性选择分析表明，LA- 基因组的进化速度较慢。我们呼吁在人类和 LA 之间进行比较微生物和泛基因组研究，这有助于进一步了解毒力的进化，从而为未来的微生物诊断和药物发现提供信息。
