Unable to find this E coli genome

Question

[pomodoro_sinensis]

Hello,

I am trying to download the E. coli genome used by the following paper (https://science.sciencemag.org/content/early/2020/12/16/science.aba5257)

It says as follows:

...where the cDNA reads were mapped to either a combined B. subtilis – E. coli genome [ASM904v1.45 and ASM80076v1.37 from EnsemblBacteria (57)] or only...

I can find the B. subtilis genome without any problem. But I am unable to find the E. coli one. Might this be a typo?

Thanks!

Answer 1

[Mensur Dlakic]

Here is the description:

https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/

Full directory:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/

Genomic DNA:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_ASM80076v1_genomic.fna.gz

[pomodoro_sinensis]

Wow thank you!! Do you happen to know why there is no transcriptome in the full directory? (i.e. a cdna.all.fa file) Or is it me who is not finding it?

[pomodoro_sinensis]

Also, where did you click here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/

to get to the full directory?

[Mensur Dlakic]

cDNA file:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_ASM80076v1_cds_from_genomic.fna.gz

Click on FTP directory for GenBank assembly

[pomodoro_sinensis]

Thanks so much!! I know there are no introns in bacteria, but still cDNA is not the collection of CDSs, am I right? A 5' or 3'UTR is part of the cDNA but not of the CDS. Is it called CDS because it doesn't include those sequences? Or is it just the way of calling the cDNA (UTRs and CDS) in bacteria's files?

[pomodoro_sinensis]

Here is an example of a B subtilis file for cDNA (corresponding to the other genome that appears in my initial message).

ftp://ftp.ensemblgenomes.org/pub/bacteria/release-49/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/cdna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.cdna.all.fa.gz

Do you happen to know if this file different from the one you sent, or is it a matter of nomenclature?