Tan Xiaodan, Qiu Huishan, Li Feng, Cheng Dong, Zheng Xueao, Wang Bingsen, Huang Mengshu, Li Wenhao, Li Yanping, Sang Kangqi, Song Botao, Du Juan, Chen Huilan, Xie Conghua
Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.
Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
Front Microbiol. 2019 Aug 14;10:1893. doi: 10.3389/fmicb.2019.01893. eCollection 2019.
, which causes bacterial wilt in a broad range of plants, is considered a "species complex" due to its significant genetic diversity. Recently, we have isolated a new strain HA4-1 from Hong'an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between and potato.
它能在多种植物中引发青枯病，由于其显著的遗传多样性，被认为是一个“种复合体”。最近，我们从中国湖北省红安县分离出一株新菌株HA4 - 1，并鉴定其为菌系I，序列变种14M（菌系I - 14M）。有趣的是，我们发现它能在不同马铃薯基因型中引发多种病害症状，与系统发育相关菌株GMI1000相比，表现出不同的致病行为。为了解析HA4 - 1的致病机制，我们通过包括Illumina HiSeq2000、PacBio RS II和BAC末端测序在内的联合测序技术对其全基因组进行了测序。基因组组装结果显示HA4 - 1中存在一条常规染色体、一个大质粒以及一个143 kb的质粒。HA4 - 1与GMI1000之间的比较基因组分析表明，诸如分泌系统、运动性、胞外多糖（EPS）和关键调控因子等一般毒力因子具有高度保守性，但III型效应子的种类和结构存在显著差异，这可能是它们在某些马铃薯物种或基因型中致病差异的决定因素。我们鉴定出两个可能通过水平基因转移（HGT）获得的新型III型效应子。这些新型效应子与几个YopJ和XopAC家族成员具有同源性。我们将它们命名为RipBR和RipBS。值得注意的是，质粒上的RipBR拷贝是一个假基因，而大质粒上的另一个拷贝是正常的。对于RipBS，分别有三个拷贝位于大质粒和质粒中。我们的研究结果不仅通过对菌系I - 14M菌株进行测序以及报道了迄今为止该菌系中最大的质粒，丰富了种复合体的基因组信息，还揭示了III型效应子种类的变化。这将极大地有助于未来对其致病进化、宿主适应性以及该菌系与马铃薯之间相互作用的研究。
