Abstract
Rose (Rosa sp.) is an important ornamental plant in the cut flower industry around the world. This species is prone to hosting several viruses since it is propagated vegetatively, mainly by grafting (Mollov et al., 2013). In 2021, rose plants of unidentified variety with mosaic, vein yellowing, chlorotic line patterns, and interveinal chlorosis were observed in a rose plantation established in open field in Temixco, Morelos (Supplementary Figure 1). To determine the cause of symptoms was due to viral infection, nucleic acids were extracted from leaves by in-house CTAB procedure and DNase treated. A pooled RNA sample extracted from 4 symptomatic plants was sent to BGI Genomics (China) for high-throughput sequencing (HTS). A stranded mRNA library was prepared and sequenced on the DNBSEQ platform (BGI). A total number of 13,646,715 paired 150-bp clean reads were generated. The reads were assembled de novo into 79,309 contigs ranging from 78 to 15,817 nucleotides (nt) using SPAdes (Prjibelskiet et al., 2020). The contigs were subjected to BLASTx and BLASTn for annotation. A contig with a length of 8,842 nt (208x average coverage per nt) showed 90.6% identity to rose virus B (RVB) (MT473961), and was deposited in GenBank under accession number ON165234. Additionally, three contigs (ON165235-ON165237) corresponding to RNA1 (3,443 nt; 154x coverage), RNA2 (2,938 nt; 231x coverage), and RNA3 (1,897 nt; 232x coverage) of apple mosaic virus (ApMV) were identified. These contigs showed up to 98.4%, 89.7%, and 98.6% identity, respectively, to each corresponding RNA sequences of ApMV. No other viral sequence was identified from the constructed contigs. Subsequently, the presence of RVB was confirmed by RT-PCR performed with an aliquot of the pooled RNAspan style="font-family:'Times New Roman'; font-size:11pt"> with specific primers targeting the replicase and CP (Diaz-Lara et al., 2021). For ApMV, a new set of primers were designed: ApMV_RNA1F (5'-AAATCTCCCGAAAGGGCCTG-3')/ApMV_RNA1R (5'-TCACTCGTCGCATGGATGGATAGC-3'), ApMV_RNA2F (5'-TTGGTACGAGTCGTGGTTGGTTGG-3')/ApMV_RNA2R (5'-GGAAAACTGACCGCAAACCC-3'), and ApMV_RNA3F (5'-GGAGGTTAGAGGCCCGAATG-3')/ApMV_RNA3R (5'-CGCACAGGTGGTAACTCACT-3') which amplify segments of 444 bp, 546 bp, and 434 bp, respectively. The amplicons obtained for both viruses were subjected to Sanger sequencing, confirming the identity of RVB and ApMV. The sequences from the RVB replicase (ON165241) and CP (ON165240) showed 93.9% and 97.0% nt identity with an RVB isolate reported in the USA (MT473961). On the other hand, sequences from RNA1 (ON165238), RNA2, (OP413436), and RNA3 (ON165239) of ApMV had 99.2%, 89.2%, and 99% nt identity, respectively. Finally, the four symptomatic plants were individually tested by RT-PCR to identify RVB and ApMV. Interestingly, both viruses were detected in all the plants analyzed. ApMV (genus Ilarvirus) is associated with mosaic and mottling symptoms in rose (Thomas, 1984). It has been accepted that ApMV is present in rose plants in Mexico (Cardenas-Alonso, 1994), with no evidence to confirm it. RVB was identified in rose in USA, and this virus was classified as a new species of the genus Carlavirus (Diaz-Lara et al., 2021). In addition to RVB, rose virus A and rose virus C have also been reported in rose; however, the symptomatology linked to these viruses is unknown (Xing et al. 2021; Diaz-Lara et al., 2020). Recently, RVB and ApMV were reported in rose plants in Taiwan (Chen et al., 2022). To our knowledge, this is the first report of RVB and ApMV in a mixed infection in rose in Mexico.
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Claims 15
Claim · model-written summary
Symptomatic roses showed mosaic, vein yellowing, chlorotic line patterns and interveinal chlorosis.
Verbatim
e0“rose plants of unidentified variety with mosaic, vein yellowing, chlorotic line patterns, and interveinal chlorosis were observed in a rose plantation established in open field in Temixco, Morelos”
Claim · model-written summary
A rose virus B contig showed 90.6% identity to the reference.
- Interactor
- rose virus BRose virus Be0pathogen
- Outcome
- identity to rose virus B (RVB)e0
- Value
- 90.6%e0
Not reportedTaxon
Verbatim
e0“A contig with a length of 8,842 nt (208x average coverage per nt) showed 90.6% identity to rose virus B (RVB) (MT473961)”
Claim · model-written summary
Three apple mosaic virus contigs were identified.
- Interactor
- apple mosaic virus
Ilarvirus ApMVe0pathogen - Outcome
- three contigse0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“three contigs (ON165235-ON165237) corresponding to RNA1 (3,443 nt; 154x coverage), RNA2 (2,938 nt; 231x coverage), and RNA3 (1,897 nt; 232x coverage) of apple mosaic virus (ApMV) were identified”
Claim · model-written summary
The ApMV RNA1 contig had 98.4% identity to reference RNA1.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- identitye0
- Value
- 98.4%e0
- Qualifier
- RNA sequencese0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These contigs showed up to 98.4%, 89.7%, and 98.6% identity, respectively, to each corresponding RNA sequences of ApMV.”
Claim · model-written summary
The ApMV RNA2 contig had 89.7% identity to reference RNA2.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- identitye0
- Value
- 89.7%e0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These contigs showed up to 98.4%, 89.7%, and 98.6% identity, respectively, to each corresponding RNA sequences of ApMV.”
Claim · model-written summary
The ApMV RNA3 contig had 98.6% identity to reference RNA3.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- identitye0
- Value
- 98.6%e0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These contigs showed up to 98.4%, 89.7%, and 98.6% identity, respectively, to each corresponding RNA sequences of ApMV.”
Claim · model-written summary
No other viral sequence was identified in the assembled contigs.
- Outcome
- No other viral sequence was identifiede0
Not reportedTaxon
Verbatim
e0“No other viral sequence was identified from the constructed contigs.”
Claim · model-written summary
RT-PCR confirmed rose virus B presence.
Not reportedTaxon
Verbatim
e0“the presence of RVB was confirmed by RT-PCR”
Claim · model-written summary
Sanger sequencing confirmed the identity of both viruses.
- Interactor
- RVBe0pathogen
- Second interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- identity of RVB and ApMVe0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The amplicons obtained for both viruses were subjected to Sanger sequencing, confirming the identity of RVB and ApMV.”
Claim · model-written summary
The RVB replicase sequence had 93.9% nucleotide identity with a US isolate.
Not reportedTaxon
Verbatim
e0“The sequences from the RVB replicase (ON165241) and CP (ON165240) showed 93.9% and 97.0% nt identity with an RVB isolate reported in the USA (MT473961).”
Claim · model-written summary
The RVB CP sequence had 97.0% nucleotide identity with a US isolate.
Not reportedTaxon
Verbatim
e0“The sequences from the RVB replicase (ON165241) and CP (ON165240) showed 93.9% and 97.0% nt identity with an RVB isolate reported in the USA (MT473961).”
Claim · model-written summary
ApMV RNA1 had 99.2% nucleotide identity.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- nt identitye0
- Value
- 99.2%e0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“sequences from RNA1 (ON165238), RNA2, (OP413436), and RNA3 (ON165239) of ApMV had 99.2%, 89.2%, and 99% nt identity, respectively.”
Claim · model-written summary
ApMV RNA2 had 89.2% nucleotide identity.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- nt identitye0
- Value
- 89.2%e0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“sequences from RNA1 (ON165238), RNA2, (OP413436), and RNA3 (ON165239) of ApMV had 99.2%, 89.2%, and 99% nt identity, respectively.”
Claim · model-written summary
ApMV RNA3 had 99% nucleotide identity.
- Interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- nt identitye0
- Value
- 99%e0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“sequences from RNA1 (ON165238), RNA2, (OP413436), and RNA3 (ON165239) of ApMV had 99.2%, 89.2%, and 99% nt identity, respectively.”
Claim · model-written summary
Both viruses were detected in all four symptomatic rose plants.
- Interactor
- RVBe0pathogen
- Second interactor
- ApMVIlarvirus ApMVe0pathogen
- Outcome
- both viruses were detected in all the plants analyzede0
Not reportedTaxon
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the four symptomatic plants were individually tested by RT-PCR to identify RVB and ApMV. Interestingly, both viruses were detected in all the plants analyzed.”