Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
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DOI：
10.1186/1471-2164-9-204
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发表时间：
2008-05-01
期刊：
影响因子：
4.4
通讯作者：
Bogdanove AJ
中科院分区：
文献类型：
--
作者：
Salzberg SL;Sommer DD;Schatz MC;Phillippy AM;Rabinowicz PD;Tsuge S;Furutani A;Ochiai H;Delcher AL;Kelley D;Madupu R;Puiu D;Radune D;Shumway M;Trapnell C;Aparna G;Jha G;Pandey A;Patil PB;Ishihara H;Meyer DF;Szurek B;Verdier V;Koebnik R;Dow JM;Ryan RP;Hirata H;Tsuyumu S;Won Lee S;Seo YS;Sriariyanum M;Ronald PC;Sonti RV;Van Sluys MA;Leach JE;White FF;Bogdanove AJ
水稻黄单胞菌水稻致病变种（Xanthomonas oryzae pv. oryzae）引发水稻（Oryza sativa L.）白叶枯病，这是一种在世界许多地区限制这种主要农作物产量的重大病害。我们在此报道菌株PXO99A的全基因组序列，并将其与之前测序的两个菌株KACC10331和MAFF311018进行比较，这两个菌株彼此高度相似。
PXO99A的基因组是一个5,240,075碱基对的环形染色体，比其他菌株的基因组（分别为4,941,439碱基对和4,940,217碱基对）长得多，它包含5083个蛋白质编码基因，其中包括87个在KACC10331或MAFF311018中未发现的基因。PXO99A含有更多与毒力相关的类转录激活因子效应基因，并且相对于KACC10331和MAFF311018至少有10个主要的染色体重排。PXO99A包含多种插入序列元件的大量拷贝，其中这些元件的成员与10个主要重排中的7个相关。一个快速进化的CRISPR（成簇的规律间隔的短回文重复序列）区域包含了PXO99A谱系所特有的数十次噬菌体感染的证据。PXO99A在靠近复制末端还包含一个独特的、近乎完美的212千碱基的串联重复序列。
我们的研究结果为水稻黄单胞菌水稻致病变种内的基因组可塑性和快速进化提供了惊人的证据。这些比较指出了基因组变异的来源以及这种病原体的菌株特异性适应的候选因素，有助于解释从世界各地分离出的水稻黄单胞菌水稻致病变种基因型和生理小种的非凡多样性。
Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.
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