Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720.
Environ Microbiol. 2020 Jul;22(7):2625-2638. doi: 10.1111/1462-2920.14965. Epub 2020 Mar 12.
Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.
韧皮部难养菌亚种韧皮部难养菌引起葡萄藤皮尔氏病（PD），在加利福尼亚已有一个多世纪的历史。一种单一引入的基因型在全州范围内传播，导致了大规模的爆发，并破坏了葡萄产业。本研究从有症状的葡萄藤中提取了 122 个韧皮部难养菌亚种韧皮部难养菌基因组，探讨了与加利福尼亚 PD 相关的病原体遗传多样性。在该数据集中发现了 5218 个单核苷酸多态性（SNP）。发现种群遗传结构很强；分离株分为五个遗传群，分为两个谱系。核心/软核心基因组构成了总基因组的 41.2%，强调了韧皮部难养菌基因组的高遗传变异性。进行了生态位模型分析，以估计病原体在加利福尼亚的环境生态位，并确定与传播有关的关键气候因素。采用景观基因组学方法旨在将局部适应与气候因素联系起来。共发现 18 个非同义多态性受到选择压力的影响，与至少一个环境变量相关，突出了温度、降水和海拔对加利福尼亚韧皮部难养菌适应葡萄藤的作用。最后，通过反向遗传学研究了三个受正选择压力影响的基因和一个重组基因对毒力的贡献。
