Submit paired bacterial chromosome and plasmid scaffolds to NCBI?

Question

[causland]

Hi all,

First time submitting scaffold-level assemblies of a bacterial chromosome and plasmid (from same strain) to NCBI GenBank. I have been using the genome submission tool on NCBI (described here) for a WGS genome. I guess I really just want to confirm that:

1. I should use 'batch submission' since I am uploading 2 genomes (the chromosome and the plasmid)
2. Per the instructions under batch submission file assignment heading (IMPORTANT: Additional requirements for batch submissions), I need to rename the fasta sequence headers according to the formatting specified therein, and
3. I can keep the chromosome and plasmid sequences as separate fasta files, as I can delineate which file is the chromosome and which is the plasmid via BioSample metadata table or leave notes to NCBI curators (there were other directions that specified that all sequences should be in one file, but it seems that this only applies to non-WGS genomes?)

The wording is tad confusing as a first time submitter, and everyone I've talked to only submits plant genomes with BankIt...

Thanks for any and all help.