Abstract
Due to the error-prone nature of viral RNA-dependent RNA polymerases, the replication of RNA viruses results in a diversity of viral genomes harboring point mutations, deletions, insertions, and genome rearrangements. Citrus tristeza virus (CTV), a causal agent of diseases of economically important citrus species, shows intrinsic genetic stability. While the virus appears to have some mechanism that limits the accumulation of single-nucleotide variants, the production of defective viral genomes (DVGs) during virus infection has been reported for certain variants of CTV. The intra-host diversity generated during plant infection with variant T36 (CTV-T36) remains unclear. To address this, we analyzed the RNA species accumulated in the initially infected and systemic leaves of Nicotiana benthamiana plants inoculated with an infectious cDNA clone of CTV-T36, which warranted that infection was initiated by a known, well-defined sequence variant of the virus. CTV-T36 limited the accumulation of single-nucleotide mutants during infection. With that, four types of DVGs—deletions, insertions, and copy- and snap-backs—were found in all the samples, with deletions and insertions being the most common types. Hot-spots across the genome for DVG recombination and short direct sequence repeats suggest that sequence complementarity could mediate DVG formation. In conclusion, our study illustrates the formation of diverse DVGs during CTV-T36 infection. To the best of our knowledge, this is the first study that has analyzed the genetic variability and recombination of a well-defined sequence variant of CTV in an herbaceous host.
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Claims 5
Claim · model-written summary
CTV-T36 limited the accumulation of single-nucleotide mutants during infection of Nicotiana benthamiana.
- Taxon
- Nicotiana benthamiana
Nicotiana benthamianat0 - Interactor
- CTV-T36e1pathogen
- Outcome
- accumulation of single-nucleotide mutantse1
- Direction
- limitede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nicotiana benthamiana”
e1“CTV-T36 limited the accumulation of single-nucleotide mutants during infection”
Claim · model-written summary
Four types of defective viral genomes were found in all samples of CTV-T36-infected Nicotiana benthamiana.
- Taxon
- Nicotiana benthamianaNicotiana benthamianat0
- Outcome
- types of DVGse2
- Value
- four typese2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nicotiana benthamiana”
e2“four types of DVGs—deletions, insertions, and copy- and snap-backs—were found in all the samples”
Claim · model-written summary
Deletions and insertions were the most common types of defective viral genomes.
- Taxon
- Nicotiana benthamianaNicotiana benthamianat0
- Outcome
- deletions and insertions being the most common typese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nicotiana benthamiana”
e3“with deletions and insertions being the most common types”
Claim · model-written summary
Hot-spots across the genome for defective viral genome recombination were observed.
- Taxon
- Nicotiana benthamianaNicotiana benthamianat0
- Outcome
- Hot-spots across the genome for DVG recombinatione4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nicotiana benthamiana”
e4“Hot-spots across the genome for DVG recombination”
Claim · model-written summary
Sequence complementarity could mediate the formation of defective viral genomes.
- Taxon
- Nicotiana benthamianaNicotiana benthamianat0
- Outcome
- DVG formatione5
- Qualifier
- sequence complementaritye5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nicotiana benthamiana”
e5“short direct sequence repeats suggest that sequence complementarity could mediate DVG formation”