Cho Shu-Ting, Lin Chan-Pin, Kuo Chih-Horng
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan.
Front Microbiol. 2019 Sep 19;10:2194. doi: 10.3389/fmicb.2019.02194. eCollection 2019.
The periwinkle leaf yellowing (PLY) disease was first reported in Taiwan in 2005. This disease was caused by an uncultivated bacterium in the genus " phytoplasma." In subsequent years, this bacterium was linked to other plant diseases and caused losses in agriculture. For genomic investigation of this bacterium and its relatives, we conducted whole genome sequencing of a PLY phytoplasma from an infected periwinkle collected in Taoyuan. The genome assembly produced eight contigs with a total length of 824,596 bp. The annotation contains 775 protein-coding genes, 63 pseudogenes, 32 tRNA genes, and two sets of rRNA operons. To characterize the genomic diversity across populations, a second strain that infects green onions in Yilan was collected for re-sequencing analysis. Comparison between these two strains identified 337 sequence polymorphisms and 10 structural variations. The metabolic pathway analysis indicated that the PLY phytoplasma genome contains two regions with highly conserved gene composition for carbohydrate metabolism. Intriguingly, each region contains several pseudogenes and the remaining functional genes in these two regions complement each other, suggesting a case of duplication followed by differential gene losses. Comparative analysis with other available phytoplasma genomes indicated that this PLY phytoplasma belongs to the 16SrI-B subgroup in the genus, with " Phytoplasma asteris" that causes the onion yellowing (OY) disease in Japan as the closest known relative. For characterized effectors that these bacteria use to manipulate their plant hosts, the PLY phytoplasma has homologs for SAP11, SAP54/PHYL1, and TENGU. For genome structure comparison, we found that potential mobile unit (PMU) insertions may be the main factor that drives genome rearrangements in these bacteria. A total of 10 PMU-like regions were found in the PLY phytoplasma genome. Two of these PMUs were found to harbor one SAP11 homolog each, with one more similar to the 16SrI-B type and the other more similar to the 16SrI-A type, suggesting possible horizontal transfer. Taken together, this work provided a first look into population genomics of the PLY phytoplasmas in Taiwan, as well as identified several evolutionary processes that contributed to the genetic diversification of these plant-pathogenic bacteria.
长春花叶片黄化（PLY）病于2005年首次在台湾被报道。这种病害是由一种未培养的“植原体”属细菌引起的。在随后的几年里，这种细菌与其他植物病害有关，并给农业造成了损失。为了对这种细菌及其亲缘种进行基因组研究，我们对从桃园采集的一株感染长春花的PLY植原体进行了全基因组测序。基因组组装产生了8个重叠群，总长度为824,596 bp。注释包含775个蛋白质编码基因、63个假基因、32个tRNA基因和两组rRNA操纵子。为了表征不同群体间的基因组多样性，我们收集了另一株感染宜兰葱的菌株进行重测序分析。对这两个菌株的比较鉴定出337个序列多态性和10个结构变异。代谢途径分析表明，PLY植原体基因组包含两个碳水化合物代谢基因组成高度保守的区域。有趣的是，每个区域都包含几个假基因，这两个区域中剩余的功能基因相互补充，表明这是一个基因复制后发生差异基因丢失的案例。与其他可用的植原体基因组进行比较分析表明，这种PLY植原体属于该属的16SrI-B亚组，与在日本引起洋葱黄化（OY）病的“ asteris植原体”是已知的最密切亲缘种。对于这些细菌用来操纵其植物宿主的已鉴定效应子，PLY植原体具有与SAP11、SAP54/PHYL1和TENGU同源的基因。对于基因组结构比较，我们发现潜在移动单元（PMU）插入可能是驱动这些细菌基因组重排的主要因素。在PLY植原体基因组中总共发现了10个类似PMU的区域。其中两个PMU各自含有一个SAP11同源基因，一个与16SrI-B型更相似，另一个与16SrI-A型更相似，表明可能存在水平转移。综上所述，这项工作首次对台湾PLY植原体的群体基因组学进行了研究，并确定了几个导致这些植物致病细菌遗传多样化的进化过程。
