How to separate plasmid from whole complete genome

Question

[Neel]

Hi, actually i had download complete genome from ncbi and few of genome has plasmid, i don't know how to remove it, if anyone know how to separate plasmid from whole complete genome file by using any script please let me know.

[GenoMax]

Plasmids should generally be a separate entry in genome file. Can you post an example of the accession you are looking at?

[Neel]

Hi, But i had read somewhere that's complete genome have one or multiple chromosomes as well as plasmid and i also check multiple time my genome has plasmid but i don't know how to separate from bacterial genome.

Thank you for your reply

[Trivas]

Can you provide more information? For example (but not limited to): What genome did you download? What format is it in? What kind of chromosome identifiers are there?

[Neel]

Hi, i had download genebank file for example GCF_000006765.1.fna and let's suppose it has plasmid sequence inside complete genome of this file with some plasmid accession number >cp027137.1. so basically i want to separate bacterial genome and it plasmid genome in different file.

Thank you for your time.

[Istvan Albert]

The plasmid sequence would be separate from the chromosomal sequence, it is not embedded in the main genome.

Each separate DNA has a separate file.

[GenoMax]

Based on example accession @istvan posted the genome file contains 4 plasmids in addition to the main genome.

$ zgrep ">" GCF_000009725.1_ASM972v1_genomic.fna.gz 
>NC_000911.1 Synechocystis sp. PCC 6803, complete sequence
>NC_005230.1 Synechocystis sp. PCC 6803 plasmid pSYSA, complete sequence
>NC_005231.1 Synechocystis sp. PCC 6803 plasmid pSYSG, complete sequence
>NC_005229.1 Synechocystis sp. PCC 6803 plasmid pSYSM, complete sequence
>NC_005232.1 Synechocystis sp. PCC 6803 plasmid pSYSX, complete sequence

You can use a program like faSplit from Jim Kent to separate the sequences into separate files. Then choose the one that contains the full genome.

[patrickdm]

So, now I'm confused; according to https://www.ncbi.nlm.nih.gov/assembly/GCF_000006765.1, I see one chromosome and no plasmids.

I guess you were referring to Istvan's example then (https://www.ncbi.nlm.nih.gov/assembly/GCF_000009725.1).

[Neel]

Thank you for your reply, i just give this file as a example GCF_000006765.1.

[patrickdm]

Ok, then I'm wasting my poor neurons here... thanks for the clarification anyway

[GenoMax]

patrickdm I used the example that @istvan had provided to Illustrate how plasmids would appear in a genome file that NCBI provides. If the plasmid is integrated in the genome then you will need to use some sort of search strategy to identify it.

[patrickdm]

GenoMax , yes I eventually got it :) I had just looked up the accession in previous Neel's comment, and got tricked. Thanks.

Answer 1

[Istvan Albert]

The plasmids, if known, ought to be annotated for example like so:

• https://www.ncbi.nlm.nih.gov/assembly/GCF_000009725.1

Another way to tell plasmids is to find genes known to be on a plasmid or to align against known plasmid databases:

• A Curated, Comprehensive Database of Plasmid Sequences (2019)

If all you have are reads or fragmented contigs then you may need to use a tool like:

• PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads(2018)

We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k-mers and uses k-mer abundance to distinguish between plasmid and bacterial sequences. We tested the performance of PlasmidSeeker on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.

[Neel]

Hi, i am trying to run plasmidseeker and here is the error-

./plasmidseeker.pl -d /home/bvs/neelam/PlasmidSeeker/db_w20 -i /home/bvs/neelam/genome/fna/ -b P_aeruginosa_PaO1.fna -o output2 Loading database... Converting sample reads to k-mers... gt4_wordmap_new: could not mmap file ./16512089695639tmp_sample_32.list gt4_wordmap_new: could not mmap file ./16512089695639tmp_sample_32.list Error: Creating the wordmap failed! Finding coverage of bacterial isolate... gt4_wordmap_new: could not mmap file ./16512089695639tmp_sample_32.list gt4_wordmap_new: could not mmap file ./16512089695639tmp_closest_32.list Error: Creating the wordmap failed! Died at ./plasmidseeker.pl line 156.

Thank you