Computational protocol: Simultaneous Detection of Both RNA and DNA Viruses Infecting Dry Bean and Occurrence of Mixed Infections by BGYMV, BCMV and BCMNV in the Central-West Region of Mexico

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Protocol publication

[…] The size of the amplicons obtained with primer pair for BGYMV detection (707 base pair; bp) [] was similar to the PCR products obtained with the primer pair used for BCMNV detection (746 bp) []; thus, two pairs of BGYMV component A-specific primers were designed () to improve the multiplex detection of BCMV, BCMNV and BGYMV. The genomic sequences of the BGYMV component A were downloaded from the National Center for Biotechnology Information (NCBI) GenBank (Accession numbers: AF173555.1, AJ544531.1, D00200.1, DQ119824.1, L01635.1, M10070.1, M91604.1 and NC_001439.1), aligned with MegAlign V7.0.0. (DNASTAR, Madison, WI, USA), and used to design primers directed to the conserved region of the AC1 gene for Replication-associated protein (Rep) using PrimerSelect V7.0.0. (DNASTAR, Madison, WI, USA) and Oligoanalyzer []. The specificity of the designed BGYMV primers was confirmed in silico using BLASTn V2.3.0 []; the amplified PCR products were sequenced, and their identities were compared with the GenBank sequences using BLASTn. […]

Pipeline specifications

Software tools PrimerSelect, OligoAnalyzer, BLASTN
Application qPCR
Organisms Bean common mosaic virus, Bean common mosaic necrosis virus
Chemicals Silica Gel