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Senna bicapsularis: A New Natural Host of Bean Yellow Mosaic Virus in China

Author:
Qiu, Y., Zhou, Y., Zhang, S., Atta, S., Li, M., Wu, J., Li, R., Cao, M.
Source:
Plant disease 2019 v.103 no.8 pp. 2144
ISSN:
0191-2917
Subject:
Bean yellow mosaic virus, Nicotiana glutinosa, RNA, RNA-directed RNA polymerase, Vigna unguiculata, agricultural land, amino acid sequences, amino acids, chlorosis, coat proteins, genome, genomics, high-throughput nucleotide sequencing, leaves, legumes, medicinal plants, nucleotides, open reading frames, phylogeny, polyproteins, rapid amplification of cDNA ends, sap, seedlings, sequence homology, shrubs, tobacco, viruses, woody plants, China
Abstract:
Senna bicapsularis, a semi-evergreen shrub of the family Fabaceae, is often grown as an ornamental and medicinal plant in South American and tropical countries. Bean yellow mosaic virus (BYMV; genus Potyvirus, family Potyviridae) infects various cultivated and wild legumes and nonlegumes such as Liliiflorae and causes diseases in many of them (Bos et al. 1970). In May 2018, virus-like symptoms of chlorosis and mosaic were observed on the primary leaves of S. bicapsularis plants in Chongqing, China. To identify the potential viral pathogens in the diseased plants, total RNA was extracted from symptomatic leaves from three plants. A library that was constructed by rRNA-depleted samples was sequenced by using Illumina NextSeq sequencing (Mega Genomics, Beijing, China). A total of 53,413,900 paired-end clean reads of 150 bp were obtained after removing sequence adaptors and low-quality reads of the raw data with CLC Genomics Workbench 9.5 (Qiagen, Valencia, CA) and used for de novo assembly. BLAST searches of the assembled contigs against viral nucleotide and protein sequences in databases revealed the presence of only one contig (9,536 nt in length), which has the highest nucleotide sequence similarity of 94% with a BYMV isolate SW9 (GenBank accession no. KF632713). Virus-specific primers were designed in accordance with the contig sequence and used in reverse transcription polymerase chain reaction (RT-PCR) to amplify the overlapped fragments of the virus genome. The 5′ terminal sequence was determined by rapid amplification of cDNA ends (RACE Kit, Invitrogen), and 3′ terminal sequence was obtained by RT-PCR using virus-specific forward and Oligo(dT) primers. Amplicons of the expected size were gel-purified, cloned into pEASY-T1 Vector System (TransGen Biotech), and sequenced (Tian et al. 2018). The whole genome of BYMV isolate BYMV-CB1 (accession no. MK516282) is 9,535 nt, excluding the poly(A) tail, and contains a large open reading frame (ORF) spanning nucleotides 194 to 9,364. Like other isolates of BYMV, the ORF encodes a polyprotein of 3,057 amino acid residues that is cleaved to 10 proteins including RNA-dependent RNA polymerase and coat protein (CP). Phylogenetic analysis of the genomic sequences of the BYMV isolates showed that BYMV-SB1 grouped most closely with BYMV-SW9 into the BYMV phylogenetic group-II (Kehoe et al. 2014). To prove the infection of the isolate BYMV-SB1 on other leguminous and tobacco plants, we rubbed the sap of the symptomatic S. bicapsularis leaves onto two true leaves of Vigna unguiculata (20 seedlings) and Nicotiana glutinosa (12 seedlings) using phosphate-buffered saline and emery. A mild mosaic symptom developed on systemic leaves of N. glutinosa, and severe mosaic and chlorotic symptoms were observed on systemic leaves of V. unguiculata 15 days after inoculation. BYMV was detected in the symptomatic leaves by RT-PCR using two pairs of virus-specific primers (NIb-F1, 5′-CGATACAAGGTGCTTTGAGAGA-3′/NIb-R1, 5′-CATCCATCTGGCAATGACTCTA-3′; CP-F1, 5′-CATAGAAATGGCATCAGGA-3′/CP-R1, 5′-TATCAGATTGACATCTCCTGC-3′). Thirty-seven samples (30 symptomatic, seven asymptomatic) of S. bicapsularis were then collected in Chongqing of China from the natural fields and tested by RT-PCR using the primers CP-F1 and CP-R1. Results indicated that all 30 symptomatic samples were infected by BYMV, whereas none of the asymptomatic samples tested positive. These results showed a strong correlation of BYMV and the symptoms on S. bicapsularis. To the best of our knowledge, this is the first report of BYMV infecting S. bicapsularis. This shrub is a perennial woody plant that is widely grown in China, and it could be potential reservoir of BYMV in agricultural areas.
Agid:
6554744