Abstract
Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major rice disease. In Taiwan, the tropical indica type of Oryza sativa originally grown in this area is mix-cultivated with the temperate japonica type of O. sativa, and this might have led to adaptive changes of both rice host and Xoo isolates. In order to better understand how Xoo adapts to this unique environment, we collected and analyzed fifty-one Xoo isolates in Taiwan. Three different genetic marker systems consistently identified five groups. Among these groups, two of them had unique sequences in the last acquired ten spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) region, and the other two had sequences that were similar to the Japanese isolate MAFF311018 and the Philippines isolate PXO563, respectively. The genomes of two Taiwanese isolates with unique CRISPR sequence features, XF89b and XM9, were further completely sequenced. Comparison of the genome sequences suggested that XF89b is phylogenetically close to MAFF311018, and XM9 is close to PXO563. Here, documentation of the diversity of groups of Xoo in Taiwan provides evidence of the populations from different sources and hitherto missing information regarding distribution of Xoo populations in East Asia.
Highlights
Xanthomonas is a large genus in γ-proteobacteria and causes diseases on more than 400 plant species
Xanthomonas oryzae pv. oryzae (Xoo) isolates in Asia have been suggested to have evolved into five modern genetic populations by RFLP or variable-number tandem-repeat (VNTR) analysis[13,14]
38 of these primers had low resolutions in the isolates, and only 11 of them could be used for grouping. These results indicate that Xoo isolates in Taiwan are genetically close to each other
Summary
Xanthomonas is a large genus in γ-proteobacteria and causes diseases on more than 400 plant species. Xoo can cause disease in both major rice sub-species, O. sativa subsp. Rice grown in Taiwan is composed of many different varieties[15], with the temperate japonica O. sativa being the major cultivar. This type of rice in Taiwan was originally adopted from Japan in the early 20th Century and naturalized through breeding programs. The groupings based on these two methods are not sufficient to classify the local isolates, and these studies do not provide comparative information among local populations and populations in the neighboring regions[12] To address these issues, we used a robust genetic classification platform to establish the distribution patterns of Xoo clonal populations in Taiwan. Our analyses reveal the complexity of rice cultivation history and indicate that Xoo populations in Taiwan may have evolved from multi-sources and undergone a unique evolutionary path
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