Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

Fajardo, Thor Vinícius Martins; Kin, Aléxis Cardama; Nickel, Osmar

doi:10.1590/0103-8478cr20161113

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CROP PROTECTION • Cienc. Rural 47 (11) • Nov 2017 • https://doi.org/10.1590/0103-8478cr20161113 copy

Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

Variantes moleculares de Grapevine rupestris stem pitting-associated virus infectando videiras (Vitis spp.) no Brasil

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT:

Grapevine rupestris stem pitting-associated virus (GRSPaV) is one of the most common viruses of grapevine. It is involved in the graft-transmissible disease rupestris stem pitting of the rugose wood complex. The objective of the research was to perform the molecular characterization of the coat protein (CP) gene of sixteen Brazilian GRSPaV isolates aiming to determine the occurrence of molecular variants (strains) of this virus. Nine grapevine samples were evaluated, from which dsRNA was extracted. Nucleotide sequences were generated by Next generation sequencing (NGS). Fifteen complete sequences of the GRSPaV CP gene were obtained and phylogenetically analyzed. Multiple alignments of the sequences showed identities of nucleotides ranging from 82% to 99%, suggesting high variability among the CPs of Brazilian isolates. The study revealed that genetic variability of GRSPaV comprising three molecular variants is also present in Brazilian grapevine genotypes.

Key words:
GRSPaV; Foveavirus; strains; lineages; genetic variability

Authorship

Thor Vinícius Martins Fajardo ^*E-mail: thor.fajardo@embrapa.br. *Corresponding author.

Empresa Brasileira de Pesquisa Agropecuária (Embrapa Uva e Vinho), CP 130, 95701-008, Bento Gonçalves, RS, Brasil. Empresa Brasileira de Pesquisa Agropecuária (Embrapa Uva e Vinho)BrazilBento Gonçalves, RS, BrazilEmpresa Brasileira de Pesquisa Agropecuária (Embrapa Uva e Vinho), CP 130, 95701-008, Bento Gonçalves, RS, Brasil.

Aléxis Cardama Kin

Universidade Estadual do Rio Grande do Sul (UERGS), Bento Gonçalves, RS, Brasil.Universidade Estadual do Rio Grande do SulBrazilBento Gonçalves, RS, BrazilUniversidade Estadual do Rio Grande do Sul (UERGS), Bento Gonçalves, RS, Brasil.

Osmar Nickel

E-mail: thor.fajardo@embrapa.br. ^*Corresponding author.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (1)
Tables (1)

Thumbnail

Figure 1
A. Pairwise nucleotide sequence identity matrix of 15 GRSPaV isolates from Brazil and 12 representative isolates from the GenBank, generated using SDT software. B. Phylogenetic relationship among GRSPaV isolates based on the multiple alignment of the complete coat protein gene nucleotide sequences of 15 isolates from Brazil and other 12 isolates and sequence variants retrieved from the GenBank. The tree was constructed by the neighbor-joining method using Kimura 2-parameter with gamma distribution (G) and 2,000 bootstrap replications implemented using MEGA 7.0.21 software package. Names of GRSPaV isolates and origins were included according to the GenBank. Reference variants for each lineage are marked with an asterisk and specific clusters (groups) are indicated as defined by NOLASCO et al. (2006NOLASCO, G. et al. Rupestris stem pitting associated virus isolates are composed by mixtures of genomic variants which share a highly conserved coat protein. Archives of Virology , v.151, p.83-96, 2006. Available from: http://link.springer.com/article/10.1007/s00705-005-0611-0>. Accessed: June 26, 2017.
http://link.springer.com/article/10.1007... ) or MENG et al. (2006MENG, B. et al. Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties. Journal of General Virology, v.87, p.1725-1733, 2006. Available from: http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.81533-0>. Accessed: June 26, 2017.
http://jgv.microbiologyresearch.org/cont... ). Bar: number of nucleotide substitutions per site.

Thumbnail

Table 1
Information about sequences of GRSPaV included in study and available in GenBank.

Figure 1 A. Pairwise nucleotide sequence identity matrix of 15 GRSPaV isolates from Brazil and 12 representative isolates from the GenBank, generated using SDT software. B. Phylogenetic relationship among GRSPaV isolates based on the multiple alignment of the complete coat protein gene nucleotide sequences of 15 isolates from Brazil and other 12 isolates and sequence variants retrieved from the GenBank. The tree was constructed by the neighbor-joining method using Kimura 2-parameter with gamma distribution (G) and 2,000 bootstrap replications implemented using MEGA 7.0.21 software package. Names of GRSPaV isolates and origins were included according to the GenBank. Reference variants for each lineage are marked with an asterisk and specific clusters (groups) are indicated as defined by NOLASCO et al. (2006NOLASCO, G. et al. Rupestris stem pitting associated virus isolates are composed by mixtures of genomic variants which share a highly conserved coat protein. Archives of Virology , v.151, p.83-96, 2006. Available from: http://link.springer.com/article/10.1007/s00705-005-0611-0>. Accessed: June 26, 2017.
http://link.springer.com/article/10.1007... ) or MENG et al. (2006MENG, B. et al. Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties. Journal of General Virology, v.87, p.1725-1733, 2006. Available from: http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.81533-0>. Accessed: June 26, 2017.
http://jgv.microbiologyresearch.org/cont... ). Bar: number of nucleotide substitutions per site.

Table 1 Information about sequences of GRSPaV included in study and available in GenBank.

Country^*	Genotypes	Isolate	GenBank accessions	Nucleotide identity with sequence variant	Variant lineage
RS-Brazil	V. vinifera cv. Cabernet Sauvignon	CS-BR	KT008367	BS (96%)	BS
RS-Brazil	V. vinifera cv. Cabernet Sauvignon	VVCS2	KT008368	3138-07 (96%)	SG1
RS-Brazil	V. flexuosa	VF1	KT008369	BS (97%)	BS
RS-Brazil	V. flexuosa	VF2	KT008370	RSPaV-1 (99%)	RSPaV-1
RS-Brazil	V. labrusca cv. Isabel	VLIS1	KT008371	BS (95%)	BS
RS-Brazil	V. labrusca cv. Isabel	VLIS2	KT008372	BS (92%)	BS
SP-Brazil	V. labrusca cv. Isabel	VLIS3	KT008373	BS (99%)	BS
SP-Brazil	V. labrusca cv. Isabel	ISA-BR	KT008374	RSPaV-1 (99%)	RSPaV-1
SP-Brazil	V. gigas	VG	KT008375	RSPaV-1 (99%)	RSPaV-1
PE-Brazil	V. vinifera cv. Syrah	VVSY1	KT008376	BS (95%)	BS
PE-Brazil	V. vinifera cv. Syrah	VVSY2	KT008377	PG (92%)	RSPaV-1
PE-Brazil	V. vinifera cv. Tempranillo	TEMP-BR	KT008378	3138-07 (96%)	SG1
RS-Brazil	V. vinifera cv. Italia	VVIT	KT008379	BS (90%)	?
RS-Brazil	V. vinifera cv. CG90450	VVCG1	KT008380	BS (96%)	BS
RS-Brazil	V. vinifera cv. CG90450	VVCG2	KT008381	3138-07 (90%)	?
RS-Brazil	V. berlandieri x V. rupestris cv. 110R	VN-BR	KY321511**	PG (99%)	---
USA	V. riparia	RSPaV-1	NC_001948	--	RSPaV-1
Italy	V.vinifera cv. Moscato Giallo	GRSPaV-MG	FR691076	--	SG1
USA	V.vinifera cv. Syrah	GRSPaV-SY	AY368590	--	SY
Canada	Vitis sp. cv. Bertille Seyve 5563	GRSPaV-BS	AY881627	--	BS
USA	Vitis vinifera cv. Pinot Noir	GRSPaV-PN	AY368172	--	PN
USA	grapevine	GRSPaV	AF026278	--	RSPaV-1
USA	V. rupestris cv. St. George	GRSPaV-SG1	AY881626	--	SG1
Canada	V. vinifera	3138-07	JX559646	--	SG1
Italy	V. vinifera cv. Pinot Gris	PG	HE591388	--	RSPaV-1
USA	V. riparia cv. Grande Glabre	GRSPaV-GG	JQ922417	--	RSPaV-1
Portugal	V. sylvestris	Vs279-2	AY927684	--	SY
USA	V. vinifera	GRSPaV-WA	KC427107	--	SG1

^*The Brazilian States of Rio Grande do Sul (RS), São Paulo (SP) and Pernambuco (PE), ^**partial CP gene and “?” not defined.

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Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

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[1] E-mail: thor.fajardo@embrapa.br. ^*Corresponding author.