Kalaivanan N S, Ghoshal Thungri, Lakshmi M Amrutha, Mondal Kalyan K, Kulshreshtha Aditya, Singh Kajol B M, Thakur Jithendra K, Supriya P, Bhatnagar Seema, Mani Chandra
Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.
Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India.
3 Biotech. 2023 Jun;13(6):187. doi: 10.1007/s13205-023-03596-x. Epub 2023 May 13.
pv. (Xoo) is a pathogen of concern for rice growers as it limits the production potential of rice varieties worldwide. Due to their high genomic plasticity, the pathogen continues to evolve, nullifying the deployed resistance mechanisms. It is pertinent to monitor the evolving Xoo population for the virulent novel stains, and the affordable sequencing technologies made the task feasible with an in-depth understanding of their pathogenesis arsenals. We present the complete genome of a highly virulent Indian Xoo strain IXOBB0003, predominantly found in northwestern parts of India, by employing next-generation sequencing and single-molecule sequencing in real-time technologies. The final genome assembly comprises 4,962,427 bp and has 63.96% GC content. The pan genome analysis reveals that strain IXOBB0003 houses total of 3655 core genes, 1276 accessory genes and 595 unique genes. Comparative analysis of the predicted gene clusters of coding sequences and protein count of strain IXOBB0003 depicts 3687 of almost 90% gene clusters shared by other Asian strains, 17 unique to IXOBB0003 and 139 CDSs of IXOBB0003 are shared with PXO99. AnnoTALE-based studies revealed 16 TALEs conferred from the whole genome sequence. Prominent TALEs of our strain are found orthologous to TALEs of the Philippines strain PXO99. The genomic features of Indian Xoo strain IXOBB0003 and in comparison with other Asian strains would certainly contribute significantly while formulating novel strategies for BB management.
The online version contains supplementary material available at 10.1007/s13205-023-03596-x.
稻黄单胞菌（Xoo）是水稻种植者关注的病原体，因为它限制了全球水稻品种的生产潜力。由于其高度的基因组可塑性，该病原体不断进化，使已部署的抗性机制失效。监测不断进化的Xoo种群中的毒性新菌株至关重要，而经济实惠的测序技术使这项任务在深入了解其致病武器库的情况下变得可行。我们通过采用下一代测序和实时单分子测序技术，展示了一种高毒性印度Xoo菌株IXOBB0003的完整基因组，该菌株主要发现于印度西北部。最终的基因组组装包含4,962,427个碱基对，GC含量为63.96%。泛基因组分析表明，菌株IXOBB0003共有3655个核心基因、1276个辅助基因和595个独特基因。对菌株IXOBB0003编码序列的预测基因簇和蛋白质数量的比较分析显示，其他亚洲菌株共享了近90%的3687个基因簇，IXOBB0003有17个独特基因，IXOBB0003的139个编码序列与PXO99共享。基于AnnoTALE的研究揭示了从全基因组序列中获得的16个转录激活样效应因子（TALEs）。我们菌株的主要TALEs与菲律宾菌株PXO99的TALEs直系同源。印度Xoo菌株IXOBB0003的基因组特征以及与其他亚洲菌株的比较，在制定稻瘟病管理新策略时肯定会有显著贡献。
在线版本包含可在10.1007/s13205-023-03596-x获取的补充材料。
