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. 2021 Jul 20;10(7):1487.
doi: 10.3390/plants10071487.

High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms

Xudong Fan  1 , Zunping Zhang  1 , Chen Li  1 , Fang Ren  1 , Guojun Hu  1 , Baodong Zhang  1 , Yafeng Dong  1
Affiliations

High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms

Xudong Fan et al. Plants (Basel). .

Abstract

A putative new marafivirus was identified in a 'Jumeigui' grapevine exhibitting obvious vein-clearing symptoms by high-throughput sequencing, which tentatively named grapevine-associated marafivirus (GaMV). The nearly complete genomic sequence of GaMV was amplified by reverse transcription PCR, and the terminal sequences were determined using the rapid amplification of cDNA ends method. The nearly complete genome of GaMV is 6346 bp long, excluding the poly(A) tail, and shows 51.2-62.3% nucleotide identity with other members of the genera Marafivirus, Maculavirus and Tymovirus in the family Tymoviridae. Additionally, it includes five functional domains homologous to those found in members of these genera. A phylogenetic analysis showed that GaMV clustered with other species-related marafiviruses. These data support GaMV being a representative member of a novel species in the genus Marafivirus. Furthermore, GaMV was graft-transmissible and 26 of 516 (5.04%) grapevine samples from five provinces in China tested positive by reverse transcription PCR. The coat protein of GaMV isolates shared 91.7-100% and 96.7-100% identities at the nt and aa levels, respectively. The coat protein-based phylogenetic trees revealed three well-defined clusters.

Keywords: Marafivirus; grapevine; high-throughput sequencing; sequence analyses; vein-clearing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
SRNA and RNA reads mapped to the genome of grapevine-associated marafivirus (GaMV). MT, methyltransferase; Pro, protease; Hel, helicase; RdRP, RNA−dependent RNA polymerase; CP, coat protein; A(n), poly(A) tail.
Figure 2
Figure 2
Neighbor-joining phylogenetic tree generated from the genomic sequences of grapevine-associated marafivirus (GaMV) and other members of the genera Marafivirus, Maculavirus and Tymovirus in the family Tymoviridae.
Figure 3
Figure 3
Testing the transmission of grapevine-associated marafivirus (GaMV) to grapevines. (a) a grafted ‘Beta’ grapevine; (b,c) partially enlarged images of (a); (d) Reverse transcription PCR (RT-PCR) detection of GaMV in five grafted grapevines using two sets of specific primers. Lane 1–5, grafted grapevine samples; P, positive control; N, negative control; M, DNA marker DL5000 (TaKaRa).
Figure 4
Figure 4
Neighbor-joining phylogenetic tree generated using CP gene sequences of grapevine-associated marafivirus (GaMV) isolates.
Figure 5
Figure 5
Symptoms on the leaves of a ‘Jumeigui’ grapevine infected with grapevine-associated marafivirus (GaMV). (a,b) vein-clearing symptoms on GaMV-infected grapevine leaves; (c) cut seedlings propagated from the GaMV-infected plant; (d,e) enlarged images of the diseased leaves of (c).
See this image and copyright information in PMC

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