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Review
. 2022 Sep 10;23(18):10507.
doi: 10.3390/ijms231810507.

Viromes of 15 Pepper (Capsicum annuum L.) Cultivars

Yeonhwa Jo  1 , Hoseong Choi  2 , Jeong Hun Lee  3 , Sang Hyun Moh  3 , Won Kyong Cho  1
Affiliations
Review

Viromes of 15 Pepper (Capsicum annuum L.) Cultivars

Yeonhwa Jo et al. Int J Mol Sci. .

Abstract

Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in five cultivars. All the bell pepper cultivars showed severe viral disease symptoms, whereas the commercially developed hot pepper cultivars were asymptomatic or had mild symptoms. In addition, 111 complete viral segments were obtained from 7 viruses. Based on the obtained viral genomes, the genetic relationship between the identified viruses and quasispecies of BBWV2 and CMV in each pepper plant was determined. Newly designed primers for nine viruses confirmed the results of RNA sequencing. Taken together, this study, for the first time, provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing.

Keywords: Capsicum annuum; RNA sequencing; pepper; virome; virus.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Images of 10 representative pepper cultivars. Few cultivars, such as P01 and P03, did not show any visible viral disease symptoms, while all paprika plants, such as P02 and P14, displayed very severe disease symptoms, such as stunting, and abnormal growth. Most pepper cultivars displayed mild symptoms, such as chlorosis, curling, mosaic, mottling, and vein banding.
Figure 2
Figure 2
Number of identified virus-associated contigs and viruses from 15 different pepper cultivars: (A) number of viral contigs identified from each library; (B) number of viral contigs according to identified viral genome or segment; (C) number of viruses identified from each library; (D) number of pepper cultivars in which individual viruses were identified.
Figure 3
Figure 3
The proportion of viral reads in each library and the proportion of identified viruses in each library: (A) the proportion of viral reads (red color) as compared to non-viral reads (gray color); (B) the proportion of identified viruses in each library. Only viral reads assigned to the identified viruses were used for the calculation of virus proportion in each library.
Figure 4
Figure 4
The number of viral reads in each library derived from four viruses composed of multiple viral segments. The number of viral reads in each library derived from BBWV2 composed of two RNA segments (A), CMV composed of three RNA segments (B), PCV1 composed of two RNA segments (C), and PCV2 composed of two RNA segments (D).
Figure 5
Figure 5
Number of assembled viral genomes: (A) total number of viral genomes or viral segments de novo assembled from RNA sequencing; (B) number of assembled viral variants for BBWV2 in each library; (C) number of assembled viral variants for CMV in each library. For viruses with multiple RNA segments, the number of assembled viral genomes is indicated by each viral segment.
Figure 6
Figure 6
Phylogenetic tree of four viruses infecting pepper cultivars; BWYV, BPEV, PCV1, and PCV2: (A) phylogenetic tree of complete genome sequences of BWYV (A), BPEV (B), PCV1 RNA1 segment (C), PCV1 RNA2 segment (D), PCV2 RNA1 segment (E), and PCV2 RNA2 segment (F). Red-colored boxes indicate the assembled viral genome obtained from this study.
Figure 7
Figure 7
Phylogenetic tree of viruses, PVY, CMV and BBWV2, infecting pepper cultivars: phylogenetic tree of complete genome sequences of PVY (A), BBWV2 RNA1 segment (B), BBWV2 RNA2 segment (C). CMV RNA1 segment (D), CMV RNA2 segment (E), CMV RNA3 segment (F). The viral genome sequences in (A,B) derived from this study were indicated by red-colored boxes.
Figure 8
Figure 8
Detection of viruses infecting pepper plants by RT-PCR: (A) RT-PCR results using 18S rRNA specific primers to confirm the quality of extracted total RNAs. RT-PCR results using specific primers for CMV (B), BBWV2 (C), BWYV (D), BPEV (E), HPEV (F), PCV1 (G), PMMoV (H), PepMoV (I), and TSWV (J). C indicates positive control. The same total RNAs used for RNA sequencing were used for RT-PCR. The number with the virus name indicates the expected size of the RT-PCR amplicon. PC and NC indicate positive and negative controls, respectively.
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