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Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations

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Abstract
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).
Keywords
Columnea latent viroid, population study, quasi-species, mutations, viroid secondary structure, amplicon sequencing, viroid-host interaction, high-throughput sequencing, variant analysis, GENETIC DIVERSITY, SPINDLE, REPLICATION, RNA, TOMATO, PSTVD, PROTEIN, VARIABILITY, INFECTION, HAIRPIN

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MLA
Tangkanchanapas, Parichate, et al. “Whole-Genome Deep Sequencing Reveals Host-Driven in-Planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 21, no. 9, 2020, doi:10.3390/ijms21093262.
APA
Tangkanchanapas, P., Haegeman, A., Ruttink, T., Höfte, M., & De Jonghe, K. (2020). Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 21(9). https://doi.org/10.3390/ijms21093262
Chicago author-date
Tangkanchanapas, Parichate, Annelies Haegeman, Tom Ruttink, Monica Höfte, and Kris De Jonghe. 2020. “Whole-Genome Deep Sequencing Reveals Host-Driven in-Planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 21 (9). https://doi.org/10.3390/ijms21093262.
Chicago author-date (all authors)
Tangkanchanapas, Parichate, Annelies Haegeman, Tom Ruttink, Monica Höfte, and Kris De Jonghe. 2020. “Whole-Genome Deep Sequencing Reveals Host-Driven in-Planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 21 (9). doi:10.3390/ijms21093262.
Vancouver
1.
Tangkanchanapas P, Haegeman A, Ruttink T, Höfte M, De Jonghe K. Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2020;21(9).
IEEE
[1]
P. Tangkanchanapas, A. Haegeman, T. Ruttink, M. Höfte, and K. De Jonghe, “Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations,” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 21, no. 9, 2020.
@article{8672346,
  abstract     = {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).},
  articleno    = {3262},
  author       = {Tangkanchanapas, Parichate and Haegeman, Annelies and Ruttink, Tom and Höfte, Monica and De Jonghe, Kris},
  issn         = {1422-0067},
  journal      = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
  keywords     = {Columnea latent viroid,population study,quasi-species,mutations,viroid secondary structure,amplicon sequencing,viroid-host interaction,high-throughput sequencing,variant analysis,GENETIC DIVERSITY,SPINDLE,REPLICATION,RNA,TOMATO,PSTVD,PROTEIN,VARIABILITY,INFECTION,HAIRPIN},
  language     = {eng},
  number       = {9},
  pages        = {17},
  title        = {Whole-genome deep sequencing reveals host-driven in-planta evolution of Columnea Latent Viroid (CLVd) quasi-species populations},
  url          = {http://dx.doi.org/10.3390/ijms21093262},
  volume       = {21},
  year         = {2020},
}

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