Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line

Abstract

Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15–39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

“…Our study supports that −ssRNA viruses, such as emaraviruses, can be detected by HTS of enriched dsRNA but with a significantly reduced efficiency. More recently, HTS of dsRNA derived from a transgenic line of common bean resistant to bean golden mosaic virus but with virus-like symptoms had a lower sequencing coverage for negative-sense RNA viruses, such as a putative cytorhabdovirus, when compared to samples with positive-sense RNA viruses, such as comovirus and carlavirus [60].…”

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

“…The sequences and characteristics of all primers used in this study are summarized in Table S1 . To determine the complete genome sequence of BaCV-Luz, first we determined the 5′ and 3′ ends by rapid amplification of cDNA ends (RACE) as previously described [ 6 , 12 , 13 ]. Next, based on the genome sequence of BaCV-GO [ 6 ] and BaCV-Luz leader and trailer sequences, primers were designed to amplify the virus genome by RT-PCR in six fragments overlapping in at least 150 nt.…”

“…Bean-associated cytorhabdovirus (BaCV) was identified in transgenic bean golden mosaic virus (BGMV)-resistant common bean lines [ 6 ]. The BaCV genome has a 3′-N-P-M-G-L-5′ [nucleocapsidprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and RNA-dependent RNA polymerase (RdRp) protein (L)] organization that is typical of rhabdoviruses and between P and M, the BaCV genome encodes two accessory genes, P3 and P4 [ 6 ]. A closely related virus with a genome sequence identity of 97% named papaya virus E (PpVE) has been reported from papaya plants in Ecuador [ 7 ].…”

Molecular and biological properties of two putative new cytorhabdoviruses infecting Trifolium pratense

“…However, knowledge about rhabdoviruses infecting plants of the Fabaceae family is limited. A bean‐infecting isolate of papaya cytorhabdovirus (Alves‐Freitas et al , ; Bejerman & Dietzgen, ) and a nucleorhabdovirus infecting Lotus corniculatus (Debat & Bejerman, ) have recently been characterized. A cytorhabdovirus, alfalfa dwarf virus (ADV), and a nucleorhabdovirus, alfalfa‐associated nucleorhabdovirus, were detected in alfalfa ( Medicago sativa ) in Argentina (Bejerman et al , ) and in Austria (Gaafar et al , ), respectively.…”