Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations

Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe

Onderzoeksoutput: Bijdrage aan tijdschriftA1: Web of Science-artikelpeer review


Columnea latent viroid (CLVd) is one of the most serious tomato diseases. In general, viroids have high mutation rates. This generates a population of variants (so-called quasi-species) that co-exist in their host and exhibit a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with a sample-specific index sequence to amplify libraries. An infectious clone of a CLVd isolate Chaipayon-1 was inoculated on different solanaceous host plants. Six replicates of the amplicon sequencing results showed very high reproducibility. On average, we obtained 133,449 CLVd reads per PCR-replicate and 79 to 561 viroid sequence variants, depending on the plant species. We identified 19 major variants (>1.0% mean relative abundance) in which a total of 16 single-nucleotide polymorphisms (SNPs) and two single nucleotide insertions were observed. All major variants contained a combination of 4 to 6 SNPs. Secondary structure prediction clustered all major variants into a tomato/bolo maka group with four loops (I, II, IV and V), and a chili pepper group with four loops (I, III, IV and V) at the terminal right domain, compared to the CLVd Chaipayon-1 which consists of five loops (I, II, III, IV and V).
Oorspronkelijke taalEngels
TijdschriftInternational Journal of Molecular Sciences
Pagina's (van-tot)3262
Aantal pagina’s17
PublicatiestatusGepubliceerd - 1-mei-2020


  • B390-gewasbescherming
  • B390-fytopathologie
  • Virology
  • viroids
  • quasi-species
  • Amplicon sequencing
  • Columnea latent viroid
  • High-throughput sequencing
  • Host interaction
  • Mutations
  • Population study
  • Quasi-species
  • Variant analysis
  • Viroid
  • Viroid secondary structure

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