This project explored the genomic diversity inside an argentinian (ARG-M) isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV).
A consensus genome sequence for SfMNPV ARGM-M was assembled (assembly/genome.fa) with Megahit from a subset of Illumina reads. Single nucleotide and structural variants were discovered through Illumina deep sequencing together with LoFreq, Delly and Lumpy as variant callers (variants_calling/snv_report, variants_calling/delly_sv.bcf and variants_calling/lumpy-sv.vcf).
All SfMNPV sequenced isolates were aligned using MAFFT with default settings (isolates_diversity/genomes.aln.fna) and single polymorphisms (isolates_diversity/snp.vcf) were extracted with SNP-sites. Additionally, a maximum likelihood phylogeny (isolates_diversity/phylogeny.treefile) was reconstructed with IQ-TREE.
Coding sequences genetic diversity was compared (viz/panels/cds_diversity.svg) using the missense mutations within and between SfMNPV isolates (viz/circos/gene_missense_mutations.csv).
BLASTp search results (molecular_evolution/sf29_blast.xml), phylogenetic reconstruction (molecular_evolution/sf29.aln.faa.treefile) and HyPhy evolutionary rate inferences (FEL, MEME and aBSREL) are provided for the putative collagenase sf29.