Genetic Variation Analysis of Grapevine Leafroll-Associated Virus 1 and 2 in Using Improved

Table 1S. Grapevine samples that tested positive for GLRaV-1 using RT-PCR and RT-nPCR.

Origin / Sample / Host species, Type / L1A/1B / G1-CP-L/R / G1-nCP-L/R / L1HSP-L/R / L1HSPn-L/R
Anhui / Kyoho / V. Vinifera-V .labrusca, Table grape / + / +
Beijing / Christmas Rose / Vitis vinifera L.,Table grape / +
Muscat Hamburg / Vitis vinifera L.,Table grape / +
Gansu / Italian Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Zuirenxiang / V. vinifera-V. labrusca, Table grape / +
Hebei / Cabernet Sauvignon / Vitis vinifera L., Wine grape / +
Kyoho / V. vinifera-V. labrusca, Table grape / +
Liaoning / Crimson Seedless / Vitis vinifera L., Table grape / + / + / +
Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Cabernet Sauvignon / Vitis vinifera L., Wine grape / +
Kishmish / Vitis vinifera L., Table grape / + / + / + / +
Qiaowushen / unknow / + / + / + / +
Muscat violet common / Vitis vinifera L., Table grape / + / + / +
Millennium / Vitis vinifera L., Wine grape / + / + / + / +
Hongshuangwei / Vitis vinifera L., Table grape / + / + / + / +
Madeleine Angevine / Vitis vinifera L., Table grape / + / + / + / +
Unknow / unknow / + / + / + / +
Qiaowushen / unknow / + / + / + / + / +
Kyptcent / Vitis vinifera L., Table grape / + / + / +
Kyptcent / Vitis vinifera L., Table grape / + / + / + / + / +
Beda / Vitis labrusca，Rootstock / +
Beda / Vitis labrusca，Rootstock / + / + / + / +
Beda / Vitis labrusca，Rootstock / + / +
Beda / Vitis labrusca，Rootstock / +
Ningxia / Chardonnay / Vitis vinifera L., Wine grape / + / + / + / + / +
Shandong / Italian Riesling / Vitis vinifera L., Wine grape / + / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / +
Beibinghong / V. amurensis-V. vinifera.Wine grape / +
Beibinghong / V. amurensis-V .vinifera.Wine grape / +
Beibinghong / V. amurensis-V. vinifera.Wine grape / +
Italian Riesling / Vitis vinifera L., Wine grape / +
Italian Riesling / Vitis vinifera L., Wine grape / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / +
Italian Riesling / Vitis vinifera L., Wine grape / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Italian Riesling / Vitis vinifera L., Wine grape / + / + / + / +
Shanghai / Tamina / Vitis vinifera L., Table grape / +
Sichuan / Red Globe / Vitis vinifera L., Table grape / +
Xijiang / Red Globe / Vitis vinifera L., Table grape / + / + / +
Thompson Seedless / Vitis vinifera L., Table grape / +
Red Globe / Vitis vinifera L., Table grape / +
Total / 15 / 12 / 36 / 22 / 35

Table 2S. Prevalence and distribution of GLRaV-1 in grapevines in China.

Origin / No. samples
tested / No. positive for
GLRaV-1
Liaoning / 43 / 17
Shandong / 35 / 18
Beijing / 15 / 2
Xinjiang / 10 / 3
Ningxia / 8 / 1
Hebei / 5 / 2
Shanghai / 4 / 1
Tianjing / 4 / 0
Gansu / 2 / 2
Yunnan / 2 / 0
Anhui / 1 / 1
Guangxi / 1 / 0
Sichuan / 1 / 1
Fujian / 1 / 0
Total / 132 / 48

Table 3S. Genetic distances between and within variant groups of GLRaV-1 CP genes.

Phylogroup / Between groups / Within groups
Group1 / 0.046±0.005
Group2 / 0.174 ±0.022 / 0.047±0.005
Group3 / 0.116±0.015 / 0.175±0.024 / 0.029±0.004
Group4 / 0.131±0.018 / 0.187±0.027 / 0.133±0.020 / 0.006±0.002
Group5 / 0.125±0.016 / 0.198±0.028 / 0.122±0.018 / 0.096±0.015 / 0.027±0.007
Group6 / 0.116±0.015 / 0.173±0.023 / 0.110±0.016 / 0.098±0.014 / 0.092±0.014 / 0.037±0.006
Group7 / 0.150±0.018 / 0.217±0.029 / 0.156±0.021 / 0.118±0.017 / 0.123±0.017 / 0.107±0.014 / 0.051±0.008
Group8 / 0.279±0.031 / 0.385±0.045 / 0.285±0.0333 / 0.278±0.034 / 0.262±0.031 / 0.245±0.028 / 0.271±0.030 / 0.112±0.017

Table 4S. Genetic distances between and within variant groups of GLRaV-1 HSP70 genes.

Phylogroup / Between groups / Within groups
Group1 / 0.050±0.006
Group2 / 0.216±0.028 / 0.043±0.006
Group3 / 0.103±0.014 / 0.203±0.028 / 0.052±0.008
Group4 / 0.124±0.017 / 0.214±0.030 / 0.117±0.017 / 0.042±0.010
Group5 / 0.118±0.017 / 0.231±0.030 / 0.117±0.016 / 0.117±0.018 / 0.060±0.012
Group6 / 0.133±0.020 / 0.228±0.031 / 0.125±0.016 / 0.113±0.018 / 0.112±0.018 / 0.072±0.016
Group7 / 0.142±0.019 / 0.267±0.036 / 0.145±0.021 / 0.145±0.021 / 0.147±0.021 / 0.141±0.021 / 0.079±0.014

Table 5S. The recombination report generated using SBP method in the CP gene sequences.

ICa / Recombinationb / IC improvementc / Breakpoint locationd / Model averaged supporte
AIC / Yes / 359.742 / 348 / 100.00%
cAIC / Yes / 273.418 / 348 / 100.00%

a, information criterion

b, was recombination inferred using this IC?

c, How many points did the recombinant model improve the IC over the base (single tree) model

d, where is the most likely breakpoint located?

e, Model averaged confidence for having recombination in the alignment

Table 6S. The KH testing report generated using GARD method in the CP gene sequences.

Breakpointa / LHS p-valueb / RHS p-valuec / Signficanced
348 / 0.00020 / 0.00020 / ***

a, Location of the significant breakpoint

b, Adjusted KH p-value that the partition to the left of this BP has a topology different from the one inferred from the partition on the right

c, Adjusted KH p-value that the partition to the right of this BP has a topology different from the one inferred from the partition on the right

d, Asterisks: * = 0.01 < P< 0.05, ** = 0.001 < P< 0.01, and *** = P< 0.001.