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Whole genome analysis and biological characterization of phage vB_XaS_HDB2 infected with Xanthomonas oryzae pv. oryzae

CHEN Hui-Ying**,HE Jia-Xin**,ZHU Bin,HUANG Shi-Xuan,ZHOU Xing-You,WU Jun-Quan,YANG Mei-Yan*   

  1. College of Food Science, South China Agricultural University / Guangdong Provincial Key Laboratory of Food Quality and Safety, Guangzhou 510642, Guangdong, China
  • Received:2024-04-07 Revised:2025-04-27 Accepted:2025-04-27 Published:2025-05-16
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (32202194), the Guangdong Key Areas Research and Development Program Project (2022B0202110001), and the Guangzhou Key Research and Development Program Agricultural and Social Development Science and Technology Project (SL2022B03J01243).

Abstract:

Bacterial leaf blight (BLB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a widespread and destructive disease that significantly reduces rice yield and threatens global food security. Currently, few chemical agents are available for BLB control, and most are either ineffective or environmentally hazardous. Therefore, there is an urgent need to develop novel, safe, and effective antibacterial alternatives. Bacteriophages, due to their high specificity against bacterial hosts, have emerged as promising biocontrol agents. In this study, we isolated a lytic phage targeting Xanthomonas, designated vB_XaS_HDB2 (HDB2), from rice and shrimp field water. Transmission electron microscopy revealed that HDB2 is a long-tailed phage with a head diameter of 48 ± 3 nm and a tail length of 166 ± 8 nm. Whole-genome sequencing showed that HDB2 has a genome size of 43,697 bp, a GC content of 54.31%, and encodes 52 open reading frames (ORFs), of which 30 were functionally annotated and grouped into four modules: DNA metabolism, lysis, packaging, and structural assembly. Notably, HDB2 carries one tRNA gene but no virulence or antibiotic resistance genes. Comparative analyses, including average nucleotide identity (ANI), protein network mapping, and phylogenetic tree construction, revealed that HDB2 belongs to the genus Septimatrevirus and is most closely related to phage vB_Xar_IVIA-DoCa8 (97.74% similarity). HDB2 was capable of lysing 52.9% (9/17) of tested Xanthomonas strains. One-step growth curve analysis indicated a latent period of 3?h, a lysis period of 5 h, and a burst size of 44 PFU per cell. HDB2 also demonstrated strong stability across a wide temperature range (4–60℃) and pH range (4–11). In vitro experiments showed that HDB2 effectively inhibited the growth of Xoo strain 2086 at multiplicities of infection (MOIs) greater than 0.1. Collectively, these results highlight the potential of HDB2 as a biocontrol agent and provide a theoretical foundation for the application of phage-based strategies in managing bacterial diseases in crops.

Key words: Xanthomonas oryzae pv. oryzae, bacterial leaf blight of rice, phage, whole genome analysis, biological characteristics

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