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通过基因组特征分析提高对‘苦楝植原体’致病性和系统发育的理解

Improving the Comprehension of Pathogenicity and Phylogeny in ' Phytoplasma meliae' through Genome Characterization.

作者信息

Fernández Franco Daniel, Yan Xiao-Hua, Kuo Chih-Horng, Marcone Carmine, Conci Luis Rogelio

机构信息

Instituto Nacional de Tecnología Agropecuaria (INTA), Centro de Investigaciones Agropecuarias (CIAP), Instituto de Patología Vegetal (IPAVE), Camino 60 cuadras km 5 ½ (X5020ICA), Córdoba X5020ICA, Argentina.

Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Unidad de Fitopatología y Modelización Agrícola (UFYMA), Camino 60 cuadras km 5 ½ (X5020ICA), Córdoba X5020ICA, Argentina.

出版信息

Microorganisms. 2024 Jan 11;12(1):142. doi: 10.3390/microorganisms12010142.

DOI:10.3390/microorganisms12010142
PMID:38257969
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10819327/
Abstract

' Phytoplasma meliae' is a pathogen associated with chinaberry yellowing disease, which has become a major phytosanitary problem for chinaberry forestry production in Argentina. Despite its economic impact, no genome information of this phytoplasma has been published, which has hindered its characterization at the genomic level. In this study, we used a metagenomics approach to analyze the draft genome of the ' P. meliae' strain ChTYXIII. The draft assembly consisted of twenty-one contigs with a total length of 751.949 bp, and annotation revealed 669 CDSs, 34 tRNAs, and 1 set of rRNA operons. The metabolic pathways analysis showed that ChTYXIII contains the complete core genes for glycolysis and a functional Sec system for protein translocation. Our phylogenomic analysis based on 133 single-copy genes and genome-to-genome metrics supports the classification as unique '. P. species' within the MPV clade. We also identified 31 putative effectors, including a homolog to SAP11 and others that have only been described in this pathogen. Our ortholog analysis revealed 37 PMU core genes in the genome of '. P. meliae' ChTYXIII, leading to the identification of 2 intact PMUs. Our work provides important genomic information for '. P. meliae' and others phytoplasmas for the 16SrXIII (MPV) group.

摘要

“苦楝植原体”是一种与苦楝黄化病相关的病原体,该病已成为阿根廷苦楝林业生产中的一个主要植物检疫问题。尽管其具有经济影响,但该植原体的基因组信息尚未公布,这阻碍了对其在基因组水平上的特征描述。在本研究中,我们采用宏基因组学方法分析了“苦楝植原体”菌株ChTYXIII的基因组草图。草图组装由21个重叠群组成,总长度为751949 bp,注释显示有669个编码序列、34个tRNA和1套rRNA操纵子。代谢途径分析表明,ChTYXIII包含糖酵解的完整核心基因和用于蛋白质转运的功能性Sec系统。我们基于133个单拷贝基因和基因组对基因组指标的系统发育基因组分析支持将其分类为MPV进化枝内独特的“苦楝植原体种”。我们还鉴定出31个假定效应子,包括一个与SAP11同源的效应子以及其他仅在该病原体中描述过的效应子。我们的直系同源分析在“苦楝植原体”ChTYXIII的基因组中揭示了37个PMU核心基因,从而鉴定出2个完整的PMU。我们的工作为“苦楝植原体”以及16SrXIII(MPV)组的其他植原体提供了重要的基因组信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/1a817c0571cd/microorganisms-12-00142-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/f858457880ec/microorganisms-12-00142-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/a8fbde0b4ab1/microorganisms-12-00142-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/0481225e4f67/microorganisms-12-00142-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/8b29a2b6d033/microorganisms-12-00142-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/d6bc1f692282/microorganisms-12-00142-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/1a817c0571cd/microorganisms-12-00142-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/f858457880ec/microorganisms-12-00142-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/a8fbde0b4ab1/microorganisms-12-00142-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/0481225e4f67/microorganisms-12-00142-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/8b29a2b6d033/microorganisms-12-00142-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/d6bc1f692282/microorganisms-12-00142-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3590/10819327/1a817c0571cd/microorganisms-12-00142-g006.jpg