Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, USA.
Department of Plant Pathology, UC Riverside, Riverside, California, USA.
Appl Environ Microbiol. 2022 Sep 22;88(18):e0122022. doi: 10.1128/aem.01220-22. Epub 2022 Sep 12.
Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most of these genes had unknown functions, but we did identify some tractable candidates, including , which encodes a beta-glucosidase that is important for Neisseria gonorrhoeae biofilm formation; , which modulates gene expression in pathogenic bacteria, and , a membrane associated histidine kinase that has roles in cell division, metabolism, and pili formation. Xylella fastidiosa causes devasting diseases to several critical crops. Because X. fastidiosa colonizes and infects many plant species, it is important to understand whether the genome of X. fastidiosa has genetic determinants that underlie specialization to specific host plants. We analyzed genome sequences of X. fastidiosa to investigate evolutionary relationships and to test for evidence of positive selection on specific genes. We found a significant signal between genome diversity and host plants, consistent with bacterial specialization to specific plant hosts. By screening for positive selection, we identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.
韧皮部坏死病菌感染了美洲的几种经济重要作物，最近也出现在了欧洲。在这里，我们使用一组反映全属多样性的基因组，基于核心和辅助基因进行了泛基因组分析，目的有二：（i）检验遗传分化与植物宿主种间的关联，（ii）鉴定可能参与军备竞赛动态的正选择基因。就前者而言，检验结果为韧皮部坏死病菌专化于植物宿主种提供了重要证据。这一观察结果有助于不断增加的文献表明，韧皮部坏死病菌谱系的系统发育历史影响宿主范围。就后者而言，我们的分析在核心基因的 5.3%（1257 个中的 67 个）和辅助基因的 5.4%（3691 个中的 201 个）的密码子上发现了正选择的证据。这些基因可能编码与植物和昆虫宿主相互作用的因子。这些基因大多数功能未知，但我们确实鉴定了一些可处理的候选基因，包括编码对淋病奈瑟菌生物膜形成很重要的β-葡糖苷酶的 ，调节致病菌基因表达的 ，以及在细胞分裂、代谢和菌毛形成中起作用的膜相关组氨酸激酶 。韧皮部坏死病菌会给几种关键作物带来毁灭性疾病。因为韧皮部坏死病菌定植和感染了许多植物种，所以了解韧皮部坏死病菌的基因组是否具有决定其对特定宿主植物专化的遗传决定因素很重要。我们分析了韧皮部坏死病菌的基因组序列，以研究进化关系并检验特定基因上正选择的证据。我们发现基因组多样性与宿主植物之间存在显著信号，这与细菌对特定植物宿主的专化一致。通过筛选正选择，我们鉴定了可能影响致病性的核心基因和辅助基因，包括参与生物膜形成的基因。
