Abstract
High-throughput RNA sequencing reveals plant viromes, but library preparation methods may bias viral detection. Here, we compared rRNA-depleted total RNA-seq and poly(A)-selected mRNA-seq using field-collected pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong) from Korean commercial fields. rRNA-depleted total RNA-seq consistently recovered more viruses, longer contigs, and complete multipartite DNA virus genomes (e.g., milk vetch dwarf virus components, tomato spotted wilt virus segments), while mRNA-seq was dominated by highly expressed polyadenylated viruses like broad bean wilt virus 2. In Jincheon pepper, mRNA-seq missed hot pepper endornavirus, pepper cryptic virus 2, and multiple milk vetch dwarf virus segments revealed by total RNA-seq. Garlic libraries showed similar patterns, with total RNA-seq additionally detecting low-titer RNA viruses likely representing contamination. rRNA-depleted total RNA-seq provides a more complete, less biased view of plant viromes and is recommended for comprehensive virus discovery and genome reconstruction, while mRNA-seq remains useful for polyadenylated virus quantification and host gene expression analysis alongside virome profiling.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 10
Claim · model-written summary
rRNA depleted sequencing recovered more viruses than mRNA sequencing.
Verbatim
e0“rRNA-depleted total RNA-seq consistently recovered more viruses, longer contigs, and complete multipartite DNA virus genomes”
e1“compared rRNA-depleted total RNA-seq and poly(A)-selected mRNA-seq using field-collected pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong)”
Claim · model-written summary
rRNA depleted sequencing recovered longer viral contigs.
Not reportedComparatorValue
Verbatim
e0“rRNA-depleted total RNA-seq consistently recovered more viruses, longer contigs, and complete multipartite DNA virus genomes”
e1“pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong)”
Claim · model-written summary
rRNA depleted sequencing recovered complete multipartite DNA virus genomes.
Not reportedComparatorValue
Verbatim
e0“rRNA-depleted total RNA-seq consistently recovered more viruses, longer contigs, and complete multipartite DNA virus genomes (e.g., milk vetch dwarf virus components, tomato spotted wilt virus segments)”
e1“pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong)”
Claim · model-written summary
mRNA sequencing was dominated by highly expressed polyadenylated viruses.
- Taxon
- peppere1
- Interactor
- broad bean wilt virus 2Broad bean wilt virus 2e0pathogen
- Outcome
- highly expressed polyadenylated virusese0
Not reportedComparatorValue
Verbatim
e0“mRNA-seq was dominated by highly expressed polyadenylated viruses like broad bean wilt virus 2”
e1“pepper leaves (Anseong and Jincheon) and garlic cloves (Hoengseong)”
Claim · model-written summary
In Jincheon pepper, mRNA sequencing missed hot pepper endornavirus.
Verbatim
e0“In Jincheon pepper, mRNA-seq missed hot pepper endornavirus, pepper cryptic virus 2, and multiple milk vetch dwarf virus segments revealed by total RNA-seq”
Claim · model-written summary
In Jincheon pepper, mRNA sequencing missed pepper cryptic virus 2.
Verbatim
e0“In Jincheon pepper, mRNA-seq missed hot pepper endornavirus, pepper cryptic virus 2, and multiple milk vetch dwarf virus segments revealed by total RNA-seq”
Claim · model-written summary
In Jincheon pepper, mRNA sequencing missed several milk vetch dwarf virus segments.
Verbatim
e0“In Jincheon pepper, mRNA-seq missed hot pepper endornavirus, pepper cryptic virus 2, and multiple milk vetch dwarf virus segments revealed by total RNA-seq”
Claim · model-written summary
Total RNA sequencing also detected low titer RNA viruses in garlic libraries, possibly contamination.
- Taxon
- Garlic
Allium sativume0 - Outcome
- low-titer RNA virusese0
- Qualifier
- likely representing contaminatione0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Garlic libraries showed similar patterns, with total RNA-seq additionally detecting low-titer RNA viruses likely representing contamination”
Claim · model-written summary
The authors recommend rRNA depleted total RNA sequencing for comprehensive virus discovery and genome reconstruction.
Verbatim
e0“rRNA-depleted total RNA-seq provides a more complete, less biased view of plant viromes and is recommended for comprehensive virus discovery and genome reconstruction”
t0“Pepper and Garlic”
Claim · model-written summary
mRNA sequencing remains useful for polyadenylated virus quantification and host gene expression analysis.
- Taxon
- Pepper and Garlict0
- Outcome
- polyadenylated virus quantification and host gene expression analysise0
Not reportedComparatorValue
Verbatim
e0“mRNA-seq remains useful for polyadenylated virus quantification and host gene expression analysis alongside virome profiling”
t0“Pepper and Garlic”