Identification and Analysis of Complete Genomic Sequences of Soybean Mosaic Virus Isolates from Atractylodes macrocephala Koidz
10.13865/j.cnki.cjbmb.2022.02.1630
- Author:
Zhen-Nan MA
1
;
De-Fu WANG
1
;
Yan-Bing NIU
1
;
Li-Yan CUI
2
;
Li ZHANG
2
;
Shu-Ting WANG
2
Author Information
1. College of Life Sciences, Shanxi Agricultural University
2. College of Grassland Science, Shanxi Agricultural University
- Publication Type:Journal Article
- Keywords:
Atractylodes macrocephala Koidz;
phylogenetic analysis;
sequence analysis;
soybean mosaic virus
- From:
Chinese Journal of Biochemistry and Molecular Biology
2022;38(4):515-526
- CountryChina
- Language:Chinese
-
Abstract:
Soybean mosaic virus (SMV) is a critical pathogen that reduces the soybean yield and seed quality worldwide, and SMV has a restricted natural host range. In this study, we used sequence-independent amplification (SIA) methods to identify the viruses that may cause the Atractylodes macrocephala Koidz disease. Results revealed that there is SMV in diseased Atractylodes macrocephala leaves, and we named this isolate as SMV-Am. To further characterize the genomic structural and phylogenetic relationships of SMV-Am, genomic dsRNA was extracted, and the genomic sequence was amplified by RT-PCR and RACE. The results of bioinformatics analysis showed that the genomic RNA of SMV-Am is 9587 nucleotides in length, which conforms to the typical characteristics of Potyvirus. According to the sequence alignment of complete nucleotide sequences, SMV-Am showed the highest level of nucleotide homology and amino acid sequences to SMV-Liaoning, 96. 57% and 98. 86%, respectively. In addition, phylogenetic analysis based on the nucleotide sequences of other SMV isolates of SMV-Am revealed that SMV-Am was most closely related to SMV-Liaoning. Then, the SMV-Am protein was further analyzed by I-TASSER and PyMOL software, revealing that the key amino acid mutations led to the structural changes of P1, HC-Pro, P3, 6K2, NIa-pro and NIb proteins, with P1 the most obvious. Finally, recombination has been detected at the position of 6560-8950 nucleotides, the main parent is the isolate SMV-XFQ012 (accession number KP710875. 1), and the secondary parent is isolate SMV-pCB301-SC15 (accession number MH919386. 1). This study is the first report of SMV in Atractylodes macrocephala Koidz, and these results are expected to provide a scientific basis for the prevention and control of SMV infection on Atractylodes macrocephala Koidz.
