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假茄科雷尔氏菌菌株RSCM的全基因组测序及基因组比较分析
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引用本文:丁善文,马紫君,蓝国兵,汤亚飞,何自福,佘小漫.假茄科雷尔氏菌菌株RSCM的全基因组测序及基因组比较分析.植物保护学报,2023,50(5):1137-1149
DOI:10.13802/j.cnki.zwbhxb.2023.2023805
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丁善文 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640  
马紫君 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640  
蓝国兵 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640  
汤亚飞 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640  
何自福 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640  
佘小漫 广东省农业科学院植物保护研究所, 广东省植物保护新技术重点实验室, 农业农村部华南果蔬绿色防控重点实验室, 广州 510640 lizer126@126.com 
中文摘要:为丰富假茄科雷尔氏菌Ralstonia pseudosolanacearum基因组数据库并探索其致病机理,以前期从南瓜上分离的菌株RSCM为研究对象,采用第二代Illumina平台与第三代PacBio平台相结合的测序技术对其进行全基因组测序,利用SMRT Link、Arrow和eggNOG等软件对测序得到的原始数据进行组装、拼接和注释,并通过比较基因组方法分析其与菌株GMI1000的差异。结果表明,菌株RSCM基因组大小约为6 000 712 bp,由3 788 542 bp的环形染色体和2 212 170 bp的环形宏质粒组成,含有5 047个编码基因,其中分别有3 579、4 240、3 171个基因获得GO、COG和KEGG数据库的注释;在菌株RSCM基因组中预测到58个tRNA、4个5S rRNA、4个16S rRNA、4个23S rRNA和4个ncRNA,含有5个前噬菌体序列和35个基因组岛。ANI分析发现研究对象与菌株GMI1000的亲缘性最近,ANI值为99.0%;基因组对比分析结果显示,与菌株GMI1000相比,菌株RSCM中存在易位、倒置、易位兼倒置的基因有571个;缺失1个Ⅱ型分泌系统的基因簇Cluster-3;且包含RipS8、RipAL、RipAP、RipAT、RipBA、RipBE、RipBM和RS_T3E_Hyp14八个特有的Ⅲ型效应蛋白。对RipBA效应蛋白进行鉴定分析,发现其具有1个糖基化位点、3个蛋白激酶C磷酸化位点和2个豆蔻酰化位点;RT-qPCR检测发现,在菌株RSCM侵染寄主过程中RipBA基因显著上调表达。表明菌株RSCM与菌株GMI1000的基因组存在差异,推测其可能与假茄科雷尔氏菌的寄主适应性和致病性有关。
中文关键词:假茄科雷尔氏菌  全基因组测序  比较基因组分析  特异基因
 
Comparative genomics analysis of Ralstonia pseudosolanacearum RSCM causing bacterial wilt of pumpkin Cucurbita maxima
Author NameAffiliationE-mail
Ding Shanwen Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
 
Ma Zijun Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
 
Lan Guobing Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
 
Tang Yafei Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
 
He Zifu Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
 
She Xiaoman Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs
Guangdong Provincial Key Laboratory of High Technology for Plant Protection
Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong Province, China 
lizer126@126.com 
Abstract:To enrich the genomic data of Ralstonia pseudosolanacearum and explore its pathogenic mechanism, the whole genome of the representative strain RSCM from pumpkin (Cucurbita maxima) was sequenced with the Illumina and PacBio platforms. The original data obtained by sequencing are assembled, spliced and annotated by softwares including SMRT Link, Arrow and eggNOG, and the genomic differences between RSCM and GMI1000 strains were compared by comparative genomics. The genome size of RSCM was 6 000 712 bp and it consisted of a 3 788 542 bp circular chromosome and a 2 212 170 bp circular megaplasmid, which contained 5 047 CDS, and 3 579, 4 240 or 3 171 genes were annotated by GO, COG and KEGG databases, respectively. In addition, 58 tRNAs, four 5S rRNAs, four 16S rRNAs, four 23S rRNAs, four ncRNAs, five prophages and 35 genomic islands were predicted in the genome of the strain RSCM. ANI analysis found that the ANI value of strain RSCM was 99.0% and closest to strain GMI1000. The comparative analysis on them showed that there were 571 genes with translocation, inversion, and both translocation and inversion in RSCM. Cluster-3 of T2SS was missing, and eight unique type Ⅲ effectors (RipS8, RipAL, RipAP, RipAT, RipBA, RipBE, RipBM and RS_T3E_Hyp14) in RSCM. In addition, RipBA had one glycosylation site, three protein kinase C phosphorylation sites and two myristoylation sites, and the expression of the gene RipBA was up-regulated in the RSCM post inoculation of its host detected by RT-qPCR. The results indicated that the genome of the strain RSCM was different from that of the strain GMI1000, which might have contributed to the host adaptability and pathogenicity of R. pseudosolanacearum.
keywords:Ralstonia pseudosolanacearum  genome  comparative genomic analysis  specific genes
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