Silva Kayla Gisela, Martins Leonor, Teixeira Miguel, Pothier Joël F, Tavares Fernando
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
Microorganisms. 2022 May 24;10(6):1078. doi: 10.3390/microorganisms10061078.
is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as . This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight -specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (, , and ) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of strains, contributing to monitoring for its presence in -colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of ; and improve the control of phytopathogenic strains.
是一种包含致病菌株和非致病菌株的细菌物种，经常与……一起在相同的寄主植物上定殖。这就需要开发一种检测和基因分型分析方法，以便在与其他黄单胞菌的微生物群落中追踪这些细菌。通过比较基因组学选择了8个特异性DNA标记（XEA1 - XEA8），并使用BLASTn、共线性分析、CG含量、密码子使用情况（CAI/eCAI值）以及与可塑性决定因素的基因组邻近性，在计算机上验证了它们的特异性和一致性。在计算机模拟中，发现所选的8个DNA标记在11个……菌株的基因组中具有特异性且保守，特别是在这些基因组中始终能找到5个DNA标记（XEA4、XEA5、XEA6、XEA7和XEA8）。针对标记XEA1（819 bp）、XEA8（648 bp）和XEA5（295 bp）的多重PCR被证明能够成功检测低至1 ng的DNA（每个PCR反应）。用三个标记（XEA5、XEA6和XEA8）和四个管家基因（……）的串联序列生成的树的拓扑结构强调了这些特征具有同等的鉴别能力，因此DNA标记适用于区分……谱系。总体而言，本研究展示了一种基于DNA标记的方法用于……菌株的检测和基因分型，有助于监测其在……定殖生境中的存在情况。本研究提出了一种选择物种特异性检测标记的工作流程。前瞻性地，该分析方法可能有助于揭示……的替代寄主物种；并改善对植物致病菌株的控制。
