WGS phylogenetic analysis

Question

[lkw222]

My company has been asked by regulatory officials to confirm the species of a filamentous fungus we use for fermentation processes. Specifically we are asked to "Provide unambiguous identification of the organism at the species level through phylogenetic analysis by comparing the whole genome sequence against related genomes."

Would someone be able to recommend a process and/or programs for doing this?

I used to do this a bit with gene sequences in grad school using clustalw and phylip. That approach doesn't seem to work for whole genome comparisons.

Thanks in advance.

Answer 1

[lkw222]

For anyone else needing an answer, what I ended up doing was using kSNP3 to do phylogenetic analysis of the fasta files from WGS of 7 genomes. It worked quickly and gave me the result I was looking for - phylogeny based on whole genome sequence data. In my case, it found over 600,000 SNPs and uses those to construct the tree.

Answer 2

[N15]

We typically use the full length 18S sequence to taxonomically identify single celled eukaryotes from the environment. If you can pull this out of your genome, you can align it to other protistan organisms using the Silva database.

https://www.arb-silva.de/

You could also look at nucleotide frequencies in your genome and compare across others, although I have less experience with this personally. This study might be helpful:

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1542-0