JIA-2019-11

2666 HU Qian-qian et al. Journal of Integrative Agriculture 2019, 18(11): 2664–2667 the IR of SbCMV-NC113 that located in the pregenomic RNA promoter and the polyadenylation signal. 3.3. Affinities to other soymoviruses and the representative members of the Caulimoviridae family The percentages sequence identity of the amino acids of encoded proteins between SbCMV-NC113 and SbCMV-JA are listed in Table 1. They shared the highest amino acid sequence identities for ORFs V, Ia, VII, and IV at 98.3, 97.4, 97.3 and 96.8%, respectively, and high identities for ORFs Ib, VI, II at 92.2, 92.2 and 92.0%, low sequence identities were observed for the unknown functions of ORF VIII (78.6%) and ORF III (75.8%). Phylogenetic analyses based on multiple alignments of the complete sequence of SbCMV-NC113, the soymoviruses and the representative members of the Caulimoviridae family were constructed using the MEGAversion 6 Software with 1000 bootstrap replicates. The resulting tree revealed that SbCMV-NC113 was most closely related to SbCMV- JA, and groups in a separate clade with the members of Soymovirus (BRRSV, PCSV and CmYLCV), while the type species of the five other genera in the Caulimoviridae family, CaMV, CsVMV, ComYMV, PVCV and RTBV were on separate branches (Fig. 1). 3.4. Field survey From 2013–2015, a total of 472 field legume samples including 161 soybean samples with SbCMV-like symptoms were collected from Jiangxi Province (Nanchang, Ji’an, Jiujiang and Ganzhou cities) and Zhejiang Province (Hangzhou, Ningbo, Wenzhou and Jiaxing cities) of China. Those 472 samples were detected by the established PCR Table 1 Predicted open reading frames (ORFs) encoded by NC113 and percentages sequence identities between NC113 and SbCMV-JA (X15828) ORFs NC113 SbCMV-JA Sequence identity (%) 1) Start (nt) Stop (nt) No. of amino acids No. of nucleotides No. of amino acids No. of nucleotides Ia 6 987 7 898 303 – 303 – 97.4 * Ib 7 901 41 116 – 116 – 92.2 * II 44 649 201 – 201 – 92.0 * III 646 1 218 190 – 192 – 75.8 * IV 1 218 2 543 441 – 441 – 96.8 * V 2 533 4 611 692 – 692 – 98.3 * VI 4 587 5 975 462 – 462 – 92.2 * VII 6 513 6 959 148 – 148 – 97.3 * VIII 2 185 2 439 84 – 84 – 78.6 * IR 5 976 6 512 – 537 – 495 85.0 # Full-length 1 8 210 – 8 210 – 8 178 91.7 # 1) * , amino acid sequence identity; # , nucleotide sequence identity. –, none. SbCMV-JA X15828.seq SbCMV-JA E02829.seq SbCMV-NC113.seq BRRSV AF404509.seq PCSV U13988.seq CmYLCV AF364175.seq PVCV U95208.seq CaMV NC001497.seq ComYMV X52938.seq CsVMV NC 001648.seq RTBV X57924.seq 100 100 100 62 97 100 80 100 0.2 Fig. 1 Neighbor-joining phylogenetic tree of the complete sequence of SbCMV-NC113 and the Caulimoviruses. The tree was generated in MEGA version 6 and bootstrapped 1 000 times. Bootstrap scores exceeding 50% are shown above the branches. The accession numbers of SbCMV-NC113, the soymoviruses and the representative members of the Caulimoviridae family are as follows: Soybean chlorotic mottle virus (SbCMV-JA, X15828, E02829 ), Blueberry red ringspot virus (BRRSV, AF404509), Peanut chlorotic streak virus (PCSV, U13988), Cestrum yellow leaf curling virus (CmYLCV, X52938 ), Cauliflower mosaic virus (CaMV, NC001497), Cassava vein mosaic virus (CsVMV, NC_001648), Commelina yellow mottle virus (ComYMV, X52938), Petunia vein clearing virus (PVCV, U95208) and Rice tungro bacilliform virus (RTBV, X57924).