Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA.
Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
BMC Genomics. 2021 May 22;22(1):373. doi: 10.1186/s12864-021-07637-8.
Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen's wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.
Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3-3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions.
The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597-2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.
柑橘衰退螺旋体由一组细菌组成，可引起柑橘、辣根、胡萝卜、芝麻等疾病，也感染广泛的观赏和杂草物种。在美国，由斑叶蝉属的 Neoaliturus tenellus 以持久增殖的方式传播，在地中海地区则由 Circulifer haematoceps 传播。叶蝉传播和病原体的广泛宿主范围是遗传多样性的驱动因素。本研究通过比较从不同宿主和时间收集的来自美国的 7 株柑橘衰退螺旋体（BR12、CC-2、C5、C189、LB 319、BLH-13 和 BLH-MB）的基因组序列与其他公开的螺旋体，从计算机上对这种多样性进行了分析。
从 NCBI 数据库中获得的 39 株螺旋体的 16S rRNA 序列的系统发育分析表明，柑橘衰退螺旋体菌株与 S. kunkelii 和 S. phoeniceum（两种其他植物病原螺旋体）形成了一个单系群。为了细化柑橘衰退螺旋体菌株之间的遗传关系，对 863 个核心直系同源序列进行了系统发育分析。聚类在一起的菌株有：CC-2 和 C5；C189 和 R8-A2；BR12、BLH-MB、BLH-13 和 LB 319。菌株 GII3-3X 仍在单独的分支中。在本研究分析的 7 株柑橘衰退螺旋体中观察到染色体的中心区域发生了序列重排。在分析的 7 株柑橘衰退螺旋体中，鉴定到 1 到 9 个质粒。从叶蝉中分离的菌株中质粒最为丰富，其次是胡萝卜、白菜、辣根和柑橘，分别从这些菌株中分离出来。所有这些柑橘衰退螺旋体菌株都含有一个与柑橘衰退螺旋体菌株 GII3-3X 的质粒 pSci6 高度相似的质粒，该质粒已知可赋予昆虫传播性。此外，在这些基因组中还鉴定到 17 到 25 个类噬菌体样元件，它们可能促进重排并有助于重复区域。
发现 7 株柑橘衰退螺旋体的基因组均包含一个单一的环状染色体，大小为 1.58 Mbp 到 1.74 Mbp，包含 1597-2232 个蛋白质编码基因。这些菌株都含有一个与 GII3-3X 菌株的 pSci6 相似的质粒，该质粒与叶蝉传播有关。在柑橘衰退螺旋体基因组中发现的噬菌体序列可能有助于扩大其宿主范围。这些发现增加了我们对柑橘衰退螺旋体遗传多样性的理解。
