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首页> 外文学位 >Comparative genomic and transcriptomic analyses of Xanthomonas citri subsp. citri and related species provides insights into virulence and host-specificity.
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Comparative genomic and transcriptomic analyses of Xanthomonas citri subsp. citri and related species provides insights into virulence and host-specificity.

机译：柑橘黄单胞菌亚种的比较基因组和转录组学分析。柠檬和相关物种提供了关于毒力和宿主特异性的见解。

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摘要

Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) has significant impact on citrus production worldwide. X. axonopodis pv. citrumelo (Xacm) is another citrus pathogen causing citrus bacterial spot disease which is geographically restricted within the state of Florida. Xcc is distinguished into different strains primarily by host range. The Asiatic strain (A) has a wide host range and is most virulent, whereas Wellington (Aw) strain has host range restricted to Mexican lime and alemow. We hypothesized that gene expression along with gene content, contributes to the difference in virulence and host range of closely related strains. We conducted comparative genomic analyses to study Xacm, A and Aw strains and transcriptomic analyses for A and Aw strains. Illumina, 454 sequencing and optical mapping were used to obtain complete genome sequences of Xacm strain F1 (4.9 Mb chromosome, no plasmid) and X. citri subsp. citri strain Aw12879 (Xcaw) (5.3 Mb chromosome and two plasmids pXcaw19 and pXcaw58). Comparative genomic analysis of Xacm to A strain showed differences in T3SS effectors, T4SS, LPS and others. In addition to pthA, putative effectors such as xopE3, xopAI and hrpW were absent in Xacm, which might be responsible for reduced virulence of this pathogen compared to XccA. We also identified unique effectors like xopC2 and xopW in Xacm that may be related to the restricted host range. Whole genome comparison of Aw to A strain, disclosed numerous genome rearrangements and insertion/deletion regions indicating genome plasticity. Protein blast revealed multiple unique genes in Aw including type III secretion system effectors xopAF and xopAG. Comparative genomic analysis showed various changes in genes related to LPS and T4SS. Furthermore, RNA-seq was used to compare expression profile of Xcaw and XccA strains in nutrient rich (NB) and plant intercellular space mimicking (XVM2) conditions using Illumina sequencing. Up-regulation of effector genes in Xcaw as compared to XccA might also contribute to its limited host range. The overexpression of genes involved in plant cell wall degradation, attachment, reactive oxygen species scavenging, nutrient transportation in XccA might contribute to its expanding of host range. Our data suggest that both gene content and gene expression contribute to difference in virulence and host-specificities of different strains.
机译：Xanthomonas citri subsp引起的柑橘溃疡病。柠檬（Xcc）对全球柑桔生产具有重大影响。 X.轴突pv。 citrumelo（Xacm）是引起柑橘细菌性斑点病的另一种柑橘病原体，在佛罗里达州范围内地理限制。 Xcc主要通过宿主范围分为不同的菌株。亚洲菌株（A）的寄主范围很广，并且最具毒性，而惠灵顿（Aw）菌株的寄主范围仅限于墨西哥石灰和阿莱莫夫。我们假设基因表达与基因含量一起导致密切相关菌株的毒力和宿主范围的差异。我们进行了比较基因组分析，以研究Xacm，A和Aw菌株以及A和Aw菌株的转录组分析。使用Illumina，454测序和光学作图来获得Xacm菌株F1的完整基因组序列（4.9 Mb染色体，无质粒）和柠檬曲霉亚种。柠檬菌株Aw12879（Xcaw）（5.3 Mb染色体和两个质粒pXcaw19和pXcaw58）。 Xacm与A菌株的比较基因组分析显示，T3SS效应子，T4SS，LPS等存在差异。除pthA以外，Xacm中不存在推定的效应子，例如xopE3，xopAI和hrpW，这可能导致该病原体的毒力比XccA降低。我们还确定了Xacm中的独特效应子，例如xopC2和xopW，可能与受限制的宿主范围有关。 Aw与A株的全基因组比较，揭示了许多基因组重排和插入/缺失区域，表明基因组可塑性。蛋白质爆炸揭示了Aw中的多个独特基因，包括III型分泌系统效应子xopAF和xopAG。比较基因组分析显示与LPS和T4SS相关的基因发生了各种变化。此外，使用Illumina测序，RNA-seq用于比较Xcaw和XccA菌株在营养丰富（NB）和植物细胞间模拟（XVM2）条件下的表达谱。与XccA相比，Xcaw中效应基因的上调也可能导致其宿主范围有限。 XccA中参与植物细胞壁降解，附着，清除活性氧，营养物质运输的基因的过度表达可能有助于其宿主范围的扩大。我们的数据表明，基因含量和基因表达都有助于不同菌株的毒力和宿主特异性的差异。

著录项

  • 作者

    Jalan, Neha.;

  • 作者单位

    University of Florida.;

  • 授予单位 University of Florida.;
  • 学科 Microbiology.;Genetics.;Plant pathology.
  • 学位 Ph.D.
  • 年度 2012
  • 页码 212 p.
  • 总页数 212
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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