Comparative genomic characterization of citrus-associated Xylella fastidiosa strains.
Comparative genomic characterization of citrus-associated Xylella fastidiosa strains.
复制标题
柑橘相关木质固醇菌株的比较基因组表征。
DOI：
10.1186/1471-2164-8-474
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发表时间：
2007-12-21
期刊：
影响因子：
4.4
通讯作者：
de Oliveira, Regina Costa
中科院分区：
文献类型：
--
作者：
da Silva, Vivian S;Shida, Claudio S;Rodrigues, Fabiana B;Ribeiro, Diogenes C D;de Souza, Alessandra A;Coletta-Filho, Helvecio D;Machado, Marcos A;Nunes, Luiz R;de Oliveira, Regina Costa
摘要木质部寄生细菌Xylella fitidiosa(XF)是引起葡萄园皮尔斯病(PD)和柑橘斑叶黄化病(CVC)的病原菌。这两种具有经济破坏性的疾病都是由这一复杂微生物组的不同菌株引起的，这促使研究人员对XF菌株进行广泛的基因组测序项目。这些序列信息与其他分子工具一起被用来估计该群体的进化历史，并提供线索来了解XF感染不同宿主的能力，从而导致各种症状。然而，尽管从XF菌株中产生了大量的信息，但这些努力中的很大一部分集中在对北美菌株的研究上，限制了我们对南美菌株基因组组成的了解--这对CVC相关菌株尤其重要。本文描述了南美XF菌株之间的首次全基因组比较，涉及6个不同的柑橘相关细菌。通过以微阵列为基础的方法进行的比较分析，使得能够识别和描述似乎是南美菌株所独有的大型移动遗传元件。此外，基于抑制消减杂交(SSH)的大规模测序工作发现了290个新的ORF，分布在这些细菌的基因组中，分布在135组同源元件中。基于微阵列的比较结果提供了关于水平转移元件活性的进一步证据，加强了它们在XF进化中作为主要介体的重要性。此外，基于微阵列的基因组图谱显示XF菌株9a5c和Fb7之间存在相似之处，这是意想不到的，因为这些微生物的分离存在地理和时间上的差异。通过SSH获得的新鉴定的ORF代表了我们目前对南美XF基因库的了解增加了大约10%，包括新的假定毒力因子，以及用于菌株鉴定的新的潜在标记。令人惊讶的是，这份新元素清单包括了以前被认为是北美菌株所特有的序列，这表明有必要修改可能用于鉴定不同XF菌株的特定标记清单。
The xylem-inhabiting bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in vineyards and citrus variegated chlorosis (CVC) in orange trees. Both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with Xf strains. This sequence information, along with other molecular tools, have been used to estimate the evolutionary history of the group and provide clues to understand the capacity of Xf to infect different hosts, causing a variety of symptoms. Nonetheless, although significant amounts of information have been generated from Xf strains, a large proportion of these efforts has concentrated on the study of North American strains, limiting our understanding about the genomic composition of South American strains – which is particularly important for CVC-associated strains. This paper describes the first genome-wide comparison among South American Xf strains, involving 6 distinct citrus-associated bacteria. Comparative analyses performed through a microarray-based approach allowed identification and characterization of large mobile genetic elements that seem to be exclusive to South American strains. Moreover, a large-scale sequencing effort, based on Suppressive Subtraction Hybridization (SSH), identified 290 new ORFs, distributed in 135 Groups of Orthologous Elements, throughout the genomes of these bacteria. Results from microarray-based comparisons provide further evidence concerning activity of horizontally transferred elements, reinforcing their importance as major mediators in the evolution of Xf. Moreover, the microarray-based genomic profiles showed similarity between Xf strains 9a5c and Fb7, which is unexpected, given the geographical and chronological differences associated with the isolation of these microorganisms. The newly identified ORFs, obtained by SSH, represent an approximately 10% increase in our current knowledge of the South American Xf gene pool and include new putative virulence factors, as well as novel potential markers for strain identification. Surprisingly, this list of novel elements include sequences previously believed to be unique to North American strains, pointing to the necessity of revising the list of specific markers that may be used for identification of distinct Xf strains.