Identification And Analysis Of Complete Genomic Sequence Of Virus Isolates Infecting Rehmannia Glutinosa And Atractylodes Macrocephala Koidz

Rehmannia glutinosa is a Scrophulariaceae perennial herbaceous plant. It is one of the famous four Huaiqing Chinese Medicines. Atractylodes macrocephala Koidz is a Compositae perennial herbaceous plant, which is as famous as Panax ginseng. It is one of ten chief exports of traditional Chinese medicines. In recent years, with the rapid increase of cultivated areas, virus infection problems and plant recession phenomenons in Rehmannia glutinosa and Atractylodes macrocephala Koidz have become increasingly serious and caused great economic losses to the related industry.In this paper, we identified the pathogens in Rehmannia glutinosa showing mosaic and curl symptoms and Atractylodes macrocephala Koidz showing mosaic and yellow symptoms in Jiangxian, Shanxi province, and then we cloned and analyze the complete sequences of the viruses.(1) Identification the pathogens that induced their disease by biological inoculation, the disease are likely to be caused by viruses.(2) dsRNAs were extracted from leaves of plant samples and used as temples in SIA, results of PCR and sequencing showed that there were Youcai mosaic virus (YoMV) and Rehmannia mosaic virus (ReMV) on Rehmannia glutinosa. At the same time, there was Broad bean wilt virus2(BBWV2) on Atractylodes macrocephala Koidz. And the name of YoMV-SX, ReMV-SX and BBWV2-Am are proposed.(3) To further characterize the YoMV-SX, ReMV-SX and BBWV-2-Am, the complete sequence of YoMV-SX, ReMV-SX and BBWV2-Am were cloned and determined. YoMV-SX comprised6304nucleotides and had a typical Tobamovirus genome organization with4ORFs. Nucleotide sequence similarity searches showed that YoMV-SX shared the highest identities(90.7%-96.0%) with YoMV, which belongs to the subgroup III of Tobamovirus. It shared lower identities (50.2%-63.3%) with the subgroup I and II. Therefore, YoMV-SX was taxonomically considered as an isolate of YoMV. Phylogenetic comparisons based on amino acid sequences of YoMV-SX and other Tobamovirus isolates showed that YoMV-SX formed an independent branch with YoMV-Wh. Therefore, YoMV-SX was most closely related to YoMV-Wh. YoMV-SX encode4kinds of protein, Replicase, Replicase read-through product, Movement Protein (MP) and Coat Protein (CP). Genetic variation of CP was the smallest, and MP was the largest. ReMV-SX comprised6395nucleotides and had a typical Tobamovirus genome organization with4ORFs. Nucleotide sequence similarity searches showed that ReMV-SX shared the highest identities(93.8%-97.0%) with ReMV, which belongs to the subgroup Ⅰ of Tobamovirus. It shared lower identities (49.8%-58.9%) with the subgroup Ⅱ and Ⅲ. Therefore, ReMV-SX was taxonomically considered as an isolate of ReMV. Phylogenetic comparisons based on amino acid sequences of ReMV-SX and other Tobamovirus isolates showed that ReMV-SX formed an independent branch with ReMV-Henan. Therefore, ReMV-SX was most closely related to ReMV-Henan. ReMV-SX encode4kinds of protein, Replicase, Replicase read-through product, MP and CP. Genetic variation of Replicase and Replicase read-through product was the smallest, MP was the largest.BBWV2-Am had a typical Fabavirus genome organization with2RNAs. RNA1comprised5949nucleotides with1ORF. Nucleotide sequence similarity searches showed that BBWV2-Am RNA1, in nucleotide identity, were from78.6%to93.3%to that of other BBWV2strains. Phylogenetic comparisons based on amino acid sequences of BBWV2-Am RNA1and other Fabavirus isolates showed that BBWV2-Am RNA1formed an independent branch with BBWV2-MB7and PatMMV-Philippines(Patchouli mild mosaic virus). Therefore, BBWV2-Am RNA1was most closely related to BBWV2-MB7and PatMMV-Philippines.BBWV2-Am RNA2comprised3548nucleotides with1ORF. Nucleotide sequence similarity searches showed that BBWV2-Am RNA2, in nucleotide identity, were from79.3%to88.5%to that of other BBWV2strains. Phylogenetic comparisons based on amino acid sequences of BBWV2-Am RNA2and other Fabaviru isolates showed that BBWV2-Am RNA2formed an independent branch with BBWV2-Rehmannia glutinosa L. Therefore, BBWV2-Am RNA2was most closely related to BBWV2-Rehmannia glutinosa L. BBWV2-Am RNA2encode3kinds of protein, Movement Protein (VP53/VP37), Large Coat Protein (LCP) and Small Coat Protein (SCP). Genetic variation of LCP was the smallest, VP53/VP37was the largest.