Download the complete nucleotide sequences of the following 11 isolates of Tomato leaf curl virus, with the NCBI reference numbers as indicated below. a) NC_003896.1 b) NC_003897.1 c) NC_010313.1 d) NC_004153.1 e) NC_003898.1 f) NC_003891.1 g) NC_055126.1 h) NC_009031.1 i) NC_009030.1 j) NC_005842.1 k) NC_005032.1 2. Run Multiple Sequence Alignment (MSA) using appropriate bioinformatics tool/program i.e. Clustal Omega. Upload or copy-paste directly all the 11 nucleotide genome sequences of the sampled ToLCV isolates. Apply default parameters. Questions: 1. How many sub-clusters or sub-grouping of the ToLCV isolates could be generated? 2. Relate the sub-grouping to the genetic relationships among isolates/between subgroups? More similar isolates, divergence or less similar/related? 3. Any isolate that represent the predicted ancestral viral genome (no evident data to support a mutation event from the root/ancestral viral genome) - Oldest isolate (genome) sequence 4. Youngest or most evolved ToLCV isolates? (have most number of mutational events/breakpoint nodes up to the divergence of the sampled isolates) 5. Other salient phylogenetics inference. E.g. distance between isolates etc.
1. Download the complete
a) NC_003896.1
b) NC_003897.1
c) NC_010313.1
d) NC_004153.1
e) NC_003898.1
f) NC_003891.1
g) NC_055126.1
h) NC_009031.1
i) NC_009030.1
j) NC_005842.1
k) NC_005032.1
2. Run Multiple Sequence Alignment (MSA) using appropriate bioinformatics tool/program i.e. Clustal Omega. Upload or copy-paste directly all the 11 nucleotide genome sequences of the sampled ToLCV isolates. Apply default parameters.
Questions:
1. How many sub-clusters or sub-grouping of the ToLCV isolates could be generated?
2. Relate the sub-grouping to the genetic relationships among isolates/between subgroups? More similar isolates, divergence or less similar/related?
3. Any isolate that represent the predicted ancestral viral genome (no evident data to support a mutation event from the root/ancestral viral genome)
- Oldest isolate (genome) sequence
4. Youngest or most evolved ToLCV isolates? (have most number of mutational events/breakpoint nodes up to the divergence of the sampled isolates)
5. Other salient phylogenetics inference. E.g. distance between isolates etc.
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