Molecular Identification And Analysis Of The Complete Genome Sequences Of Bean Common Mosaic Virus From Three Legumes

China is one of the main legnums producing countries of the world, legnums rankedsecond place just after the graminaceous plants as crops grown agriculturally. Soybeans,mung beans and hyacinth beans originated from China, and have a long history of cultivationin China. Soybeans, hyacinth beans, mung beans are widely planted in Shandong, which is amain legumes producing province.Bean common mosaic virus (BCMV), that cause particularly serious disease on legumes,is a member of the Potyvirus. BCMV has occurred in many parts of the world. In this study,we have collected leaves of soybeans, hyacinth beans, and mung beans which appeared theBCMV symptoms in Tai’an, Shandong. The registered sequences under the GenBank wereused to design primers to amplify the complete genome sequences.The complete genome sequences of BCMV isolated from soybeans, hyacinth beans,mung beans were amplified and sequenced in this study. These sequences were analyzed withgenome sequences of other BCMV strains, the result revealed that, the BCMV isolates ofsoybean, hyacinth bean, mung bean beglong to different groups in the phylogenetic trees ofthe complete genome sequences and the amino acid sequences of coat protein, BCMV-soybean (BCMV-SB) was clustered with BCMV-blackeye strains, BCMV-hyacinth beansisolates (BCMV-HB) was set between BCMV-peanut stripe virus strains (Peanut stripe virus,PStV) and other BCMV strains, BCMV-mung bean isolates (BCMV-MB) was mostly closeto BCMV strains isolated from common beans. According to the analysis results, BCMV-SB,BCMV-HB and BCMV-MB share the amino acids identities of86.3%~97.2%,85.3%~91.5%and88.3%~93.7%, when compared with other BCMV sequences, and the identities ofnucleotides were78.7%~95.6%,74%~83.6%, and78.9%~89.2%, when they were comparedwith other BCMV complete genome sequences. The identities of BCMV-SB/BCMV-HB,BCMV-SB/BCMV-MB, BCMV-HB/BCMV-MB were:82.6%,83.8%and83.4%. The aminoacids sequences of coat protein of BCMV-SB, BCMV-HB and BCMV-MB share theidentities of90.9%~99.7%,89.9%~93.7%and89.9%~95.1%when they were compared withother BCMV sequences used in this study, and the identities of BCMV-SB/BCMV-HB,BCMV-SB/BCMV-MB, BCMV-HB/BCMV-MB were:91.3%,93%and89.5%. Thenucleotides sequences of coat protein of BCMV-SB, BCMV-HB and BCMV-MB share theidentities of84.8%~98.4%,83.7%~89.9%and85.9%~92.9%when they were compared withother BCMV sequences used in this study, and the identities of BCMV-SB/BCMV-HB,BCMV-SB/BCMV-MB, BCMV-HB/BCMV-MB were:89.8%,89.8%and87.4%. According to our results, the isolates BCMV-HB and BCMV-MB are new strains of BCMV, and isolateBCMV-SB belongs to blackeye strains of BCMV.There are some signs of recombinations in BCMV-SB, BCMV-HB and BCMV-MB,when BCMV-SB, BCMV-HB, BCMV-MB were compared with other BCMV isolates. Byusing the RDP4.0and Simplot3.5.1software program, recombination sites have beendetected in the P1gene of BCMV-SB sites (P-value was less than10-13), locatingapproximately597nt and1036nt, the putative parents are BCMV-Y and BCMV-blacekey(also named BlCMV), the phylogenetic trees were created based on ether sides of the twobreakpoints, the results of the analysis show that BCMV-SB was close to BlCMV in the5’-UTR~596nt and1037to3’-UTR region, and it was close to BCMV-Y in597nt~1036ntregion, where BCMV-SB and BCMV-Y were grouped into the same branch; there were alsosome recombination sites in BCMV-HB according to the recombinant software analysis (P-value was less than10-5), the breakpoints were approximately located at8033nt and8616ntin the NIb gene, PStV-Ts and BlCMV were detected as its putative parents, it was close toPStV-Ts in the5’-UTR~8032nt and8617to3’-UTR region, and in8033nt~8616ntregion BCMV-HB was clustered with BlCMV; an apparent signal of recombinant wasdetected by recombination software (P-value was less than10-15), the recombinant pointswere located approximately at2285nt,3358nt,5350nt, respectively located in the HC-Pro,P3and CI gene, BCMV-Y and BCMV-NL1were putative parent lineages. In the5’-UTR~2285nt and3359~5350nt region, BCMV-MB shares the highest identities with BCMV-Yand was most closely in the phylogenetic tree. While in2286~3358nt and5351~3’-UTRregions BCMV-MB shares the highest identities with BCMV-NL1and was most closely inthe phylogenetic tree.