Related Experiment Videos
Sequence variability within the 3'-proximal part of the Sweet potato mild mottle virus genome
S B Mukasa1, P R Rubaihayo, J P T Valkonen
1Department of Plant Biology, Genetics Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Abstract:
Sweet potato mild mottle virus (SPMMV) is the type member of the genus Ipomovirus (family Potyviridae) and is only known to occur in East Africa. In Uganda, SPMMV is the third most prevalent virus infecting sweet potato. The sequence variability of SPMMV was studied by cloning and sequencing a 1.8-kb fragment representing the 3'-end of the genome of eight SPMMV isolates collected from different districts of Uganda. Sequence comparisons indicated 85.9-99.9% nucleotide sequence identity and 92.8-100% amino acid sequence similarity for the coat protein (CP) encoding region. The nucleotide sequence identity within the 3'-untranslated region (3' UTR) was 84.7-100%, and the region was variable in length (303-308 nucleotides) due to some deletions within the 5'-proximal part of the 3' UTR. Phylogenetic analysis of the CP amino acid sequences revealed significant clustering, indicating the existence of distinguishable sequence variants or strains. The low CP amino acid sequence similarity of SPMMV isolates with other characterised viruses of the family Potyviridae and the unusual putative proteolytic cleavage site at the NIb/CP junction further demonstrate SPMMV as a very distinct virus in the family Potyviridae.
Insights
Sweet potato mild mottle virus (SPMMV) in Uganda shows significant genetic diversity. Analysis of eight isolates reveals distinct sequence variants and strains, highlighting SPMMV as a unique virus within its family.
Area of Science:
- Plant virology
- Molecular biology
- Genetics
Background:
- Sweet potato mild mottle virus (SPMMV) is the type member of the Ipomovirus genus within the Potyviridae family.
- SPMMV is prevalent in East Africa and ranks as the third most common virus affecting sweet potatoes in Uganda.
Purpose of the Study:
- To investigate the sequence variability of SPMMV isolates from Uganda.
- To analyze the genetic diversity within the coat protein (CP) encoding region and the 3'-untranslated region (3' UTR).
Main Methods:
- Cloning and sequencing of a 1.8-kb fragment from the 3'-end of the SPMMV genome.
- Comparative analysis of nucleotide and amino acid sequences.
- Phylogenetic analysis of CP amino acid sequences.
Main Results:
- Nucleotide sequence identity ranged from 85.9-99.9% for the CP region and 84.7-100% for the 3' UTR.
- The 3' UTR showed length variation (303-308 nucleotides) due to deletions.
- Phylogenetic analysis identified distinct SPMMV sequence variants or strains.
- SPMMV isolates exhibited low sequence similarity to other Potyviridae viruses, with an unusual NIb/CP cleavage site.
Conclusions:
- SPMMV isolates in Uganda display considerable genetic variability, forming distinct phylogenetic clusters.
- The observed sequence divergence and unique features support SPMMV's distinct status within the Potyviridae family.