Retrieving an operon from scaffolds : Prokaryotic Genome

Question

[venuraherath]

Hi,

I am interested in retrieving operons from prokaryotic genomes available in NCBI with the objective of looking at their synteny. My questions is how to assemble an operon when it is scattered among different scaffolds. As an example, if i want to look at Cylindrospermopsis raciborskii devBCA operon or nif operon with other spp. Cylindrospermopsis raciborskii representative genome (genome_assembly_id=172353 , shotgun sequencing) consist of 93 scaffolds and genes of the operon are find in many scaffolds. What is the in silico procedure, I should follow in order to overcome this issue?

Thank you.

[Joe]

If you haven’t got data to close those gaps, you cannot improve on the assembly/scaffold as it stands. Are you certain that genome is at the scaffold level, or does it contain 93 contigs?

If these genes are all supposed to be within one operon, it seems strange to me that they’d be split over more than at most 2 contigs.

[venuraherath]

. It says 93 scaffolds. I was also puzzled I thought they should be in one scaffold. :(

[Joe]

I think that's actually the contig number, which this page would confirm:

In any event, do you need to use that accession specifically? There's a complete CS505 genome from PacBio at https://www.ncbi.nlm.nih.gov/assembly/GCF_001676585.1/

You might be able to gain some information by putting the genome through an actual scaffolding process, but all you'll be gaining is ordering information held together with Ns. If the sequence is missing the only thing you can do is look at another, more complete genome and hope they're similar in the areas you need,

[pltbiotech_tkarthi]

You can try https://bacteria.ensembl.org/Multi/Tools/Blast?db=core. There is zoom in and zoom out options after finding a physical location of a gene or operon and you can zoom in to findout adjacent genes or operon or domain features after having a BLASTN analysis result from the gene or fragment of interest.