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Genomic sequencing globally identifies functional genes and potential virulence-related effectors of Xanthomonas axonopodis pv. malvacearum

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Abstract

Highly virulent strains (HVS) of Xanthomonas axonopodis pathovar (pv.) malvacearum (Xam) infect all commercial cultivars of cotton, including the long-established “immune” cultivar 101-102B. Here, we present high-quality draft sequences of a highly virulent Xam strain (GSPB2388) from Sudan, and a strain of race 18 (GSPB1386) from Nicaragua, using Illumina/Solexa paired-end sequencing. The short sequence reads were assembled into 61 scaffolds for GSPB2388 (N50 of 164 kb) and 127 scaffolds for GSPB1386 (N50 of 100 kb), with draft maps of roughly 5 Mb, which contain 4,665 and 4,520 protein-coding genes, respectively. Through gene annotation and comparisons with plant pathogen proteins, 181 and 178 potential virulence-related genes, including genes encoding a major group of type III effectors, were identified from GSPB2388 and GSPB1386, respectively. The differential effectors and sequence diversity between the HVS and race 18 may enable the identification of key factors that contribute to the high virulence of HVS. Additionally, the average nucleotide identity (ANI) between Xam and Xanthomonas axonopodis pv. citri is 98.4 %, suggesting that these strains belong to the same species.

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Acknowledgments

We thank the staff of Beijing Genomics Institute of Shenzhen of China for their technical assistance with data analysis. This work was supported by a grant from the Project of Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University.

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Authors and Affiliations

  1. Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, 570228, People’s Republic of China

    Jinling Zhai, Zhihui Xia, Wei Liu, Xingyu Jiang & Xi Huang

  2. Institute of Bioscience and Technology, College of Agriculture, Hainan University, 570228, Haikou, People’s Republic of China

    Xi Huang

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  1. Jinling Zhai
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  2. Zhihui Xia
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  3. Wei Liu
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  4. Xingyu Jiang
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Correspondence to Xi Huang.

Additional information

Jinling Zhai and Zhihui Xia contributed equally to this work.

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Zhai, J., Xia, Z., Liu, W. et al. Genomic sequencing globally identifies functional genes and potential virulence-related effectors of Xanthomonas axonopodis pv. malvacearum . Eur J Plant Pathol 136, 657–663 (2013). https://doi.org/10.1007/s10658-013-0213-8

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