Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
mSphere. 2020 Apr 15;5(2):e00087-20. doi: 10.1128/mSphere.00087-20.
species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, , from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., ype 1 ecretion ystem [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and gene cluster) and adaptation (i.e., , iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.
物种主要被认为是一组感染多种植物的植物病原体。最近的分子研究揭示了潜在的新型物种和菌株的存在，这些物种和菌株遵循非致病性的生活方式。在本研究中，我们报告了来自柑橘的四个非致病性菌株的全基因组序列（NPXc）。分类基因组学揭示了令人惊讶的多样性，因为这三个分离株中的每一个都被发现是潜在的新型物种，它们共同构成了一个柑橘相关的非致病性 物种复合体（NPXc 复合体）。有趣的是，这个 NPXc 复合体与另一个来自水稻的非致病性物种 有关（NPXr）。另一方面，第四个 NPXc 分离株被发现与来自核桃的非致病性分离株有关（NPXw）；总的来说，它们形成了一个潜在的致病性 物种的分类学异常。此外，对 NPXc 分离株中特征明确的致病性簇的基因组研究揭示了特定于生活方式的基因含量动态。主要是，毒力必需基因（即 1 型分泌系统[T1SS]、T2SS 及其效应物、T3SS 及其效应物、T4SS、T6SS、粘附素和 基因簇）和适应性基因（即铁摄取和利用、黄单胞素和双组分系统）通过对包括多种生活方式的 群落的比较基因组学进行了描绘。总的来说，目前的分析表明，来自不同宿主的非致病性分离株在系统发育上趋同，并与它们的致病性对应物平行进化。因此，需要了解来自不同宿主的非致病性分离株的世界。非致病性菌株的基因组知识和资源在 属的基础和应用研究中都是非常宝贵的， 属是顶级植物病原体之一，是柑橘溃疡病的病原体。有趣的是，也有报道称与健康的柑橘植物有关。基因组时代的到来使我们能够对与柑橘和其他植物相关的 群落进行详细的进化研究。我们基于基因组的研究揭示了来自柑橘植物的非致病性 菌株的隐藏和极端菌株多样性，需要进一步进行大规模研究。这表明，来自健康柑橘植物物种的 属有一个未被探索的世界，它可能与宿主一起作为一个物种复合体共同进化，而不是作为变异的致病性物种。这些知识和基因组资源将在探索其隐藏潜力和管理致病性物种的进化研究中具有价值。
