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Updated: Dec 10, 2025
08:56
Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
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A New Method to Obtain the Complete Genome Sequence of Multiple-Component Circular ssDNA Viruses by Transcriptome
Nai-Tong Yu1,2, Yu-Liang Zhang1, Jian-Hua Wang1,2
1Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
Frontiers in Bioengineering and Biotechnology
|August 28, 2020
Summary
This study introduces a novel RNA-based transcriptome sequencing method to assemble the complete genome of Banana Bunchy Top Virus (BBTV). This approach successfully sequenced viral mRNA (vmRNA) components, offering new insights into nanovirid genome sequencing.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- Circular single-stranded DNA (ssDNA) viruses, like Banana Bunchy Top Virus (BBTV), infect diverse hosts.
- BBTV has a multi-component genome, typically sequenced at the DNA level.
- RNA-based genome sequencing methods for such viruses were previously unreported.
Purpose of the Study:
- To develop and validate an RNA-based method for sequencing the multi-component ssDNA genome of BBTV.
- To investigate the transcriptional mechanisms within the Nanoviridae family.
Main Methods:
- Transcriptome sequencing of BBTV-infected banana leaves.
- Assembly of viral mRNA (vmRNA) sequences.
- Gap-filling using reverse transcription-polymerase chain reaction (RT-PCR).
- Quantitative reverse transcription-PCR (RT-qPCR) to analyze vmRNA levels.
Main Results:
- Full-length sequences were obtained for most BBTV genomic components (DNA-R, DNA-U3, DNA-S, DNA-M, DNA-N, NewS2, Sat4) via transcriptome sequencing.
- The DNA-C component required RT-PCR for complete assembly.
- vmRNA levels in coding regions were significantly higher than non-coding regions, suggesting transcription levels influence genome assembly integrity.
Conclusions:
- A novel RNA-based approach using transcriptome sequencing is proposed for assembling nanovirid genomes.
- This method provides valuable insights into the transcriptional mechanisms of Nanoviridae, Genomoviridae, and Geminiviridae families.
- The study highlights the importance of transcription levels for understanding genome assembly in these viral families.
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