Chambers Grant A, Geering Andrew D W, Bogema Daniel R, Holford Paul, Vidalakis Georgios, Donovan Nerida J
NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia.
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland, 4001, Australia.
Arch Virol. 2024 Dec 12;170(1):12. doi: 10.1007/s00705-024-06191-4.
Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term 'quasispecies' to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (> 10% sample) variants. The composition of variants differed in samples from different plants and among tissue types of a single plant. Single-nucleotide polymorphisms (SNPs), mostly in the form of substitutions, were the primary source of variation; in this study, SNPs were observed in approximately 10% of the viroid genome. The results of the three experiments indicate that CVd-VII follows the quasispecies model as reported for other viroids and that variability occurs in viroid populations in different tissue types and host species.
类病毒以围绕一个优势变体聚集的序列变体群的形式存在于植物中，因此采用了“准种”这一术语来描述单个宿主中的类病毒群体。准种的组成可能会根据感染的时间、树冠中叶或枝的位置以及宿主物种而发生变化。本研究的主要目的是调查柑橘类病毒VII（CVd-VII）的准种概念，CVd-VII是最近发现的马铃薯纺锤块茎类病毒科的成员。进行了三个实验，以确定影响类病毒变异性的因素：（i）在柠檬植株的不同组织内；（ii）在同一物种（枸橼）的不同植株之间；（iii）在柑橘的不同物种和杂种之间。使用两组引物产生用于高通量测序的扩增子，为每个样品生成类病毒群体概况。两组引物均鉴定出的变体数量每个样品为2至13个，每个样品包含1至4个主要（>10%样品）变体。不同植株的样品以及单个植株的不同组织类型之间的变体组成有所不同。单核苷酸多态性（SNP），大多以替换的形式，是变异的主要来源；在本研究中，在约10%的类病毒基因组中观察到SNP。这三个实验的结果表明，CVd-VII遵循其他类病毒所报道的准种模型，并且类病毒群体在不同组织类型和宿主物种中会发生变异。
