Zhang Jingxin, Arif Mohammad, Shen Huifang, Sun Dayuan, Pu Xiaoming, Hu John, Lin Birun, Yang Qiyun
Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, HI, United States.
Front Plant Sci. 2022 Feb 9;13:822829. doi: 10.3389/fpls.2022.822829. eCollection 2022.
Bacterial soft rot of banana, caused by , is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other . strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish ( AAA) and Plantain ( ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.
由[病原菌名称未给出]引起的香蕉细菌性软腐病正在中国重要的香蕉种植区迅速蔓延，严重威胁香蕉生产。在本研究中，我们对2009年、2014年和2018年分别分离得到的三株典型香蕉菌株MS1（大小：4,831,702碱基对；基因组覆盖度：538倍）、MS_2014（大小：4,740,000碱基对；基因组覆盖度：586倍）和MS_2018（大小：4,787,201碱基对；基因组覆盖度：583倍）的高质量完整基因组进行了测序。为了确定它们相对于其原始宿主的基因组和表型多样性，将它们与其他[病原菌名称未给出]菌株进行了比较，包括另一株来自中国的代表性香蕉菌株MS2。测序菌株在碳源和化学底物利用、GC含量以及tRNA和rRNA区域等一般基因组特征方面相似。它们在大多数毒力决定因素方面也保守，包括编码分泌系统、植物细胞壁降解酶和胞外多糖的基因。我们进一步在预测的基因组岛（GI）中探索了它们的基因组多样性。这些基因组岛富含整合酶和转座酶，在鞭毛基因簇和几个次生代谢物基因簇中观察到一些基因组差异。在细菌素和芳基多烯（APE）色素基因簇中发现了核心生物合成模块的不同组成部分，并且来自香蕉的菌株在抗菌作用和菌落色素沉着方面表现出不同的表型。此外，成簇规律间隔短回文重复序列（CRISPR）和前噬菌体元件，如I-F型和III-A型CRISPR阵列以及MS1-P5的一个完整前噬菌体，促成了细菌的多样性。系统发育树分析和全基因组核苷酸比较证实了从香蕉分离的菌株之间的基因组差异。考虑到这些特征，MS2和MS_2014可能比MS1分化得晚，而MS_2018不同，并且在几个特征上与从其他宿主分离的国外菌株更相似。菌株MS_2018对先前被认为是中度抗性或中度敏感的香蕉品种，包括卡文迪什（AAA）和大蕉（ABB）品种，会引起严重症状。我们对基因组和表型多样性的研究引起了公众对香蕉种植区内新致病变体传播风险的关注，并支持了疾病控制预测策略的制定。
