variability in sequences of a gene

[bioinfobeginner]

Hi All!

I downloaded V1-V2 hypervariable region of 16S sequence data of Fusobacterium sequenced by 454. I was expecting taht all the reads to be identical as it is one gene of single species but the reads are different. I want to know if this should be the case that there is variability in the sequences of single gene or all the sequences should be identical.
Any kind of help will be appreciated.

Thanks!!

[Brian Bushnell]

Bacteria have multiple 16S copies, and those copies can differ substantially (by over 3%) within a single cell, depending on the species. It's rather amusing because by some metrics that makes a single cell a different species than itself.

[bioinfobeginner]

Bacteria have multiple 16S copies, and those copies can differ substantially (by over 3%) within a single cell, depending on the species. It's rather amusing because by some metrics that makes a single cell a different species than itself.

Thanks Brian for answering my question. Is there any reference that states that the variability
is over 3%. I have to quote it in a report.

[Brian Bushnell]

Thanks Brian for answering my question. Is there any reference that states that the variability
is over 3%. I have to quote it in a report.

I only remember it because it caused problems when clustering, as that 16S copy was more similar to a different species than to the other 16S of its own species. I don't remember the species name or the exact amount of difference, so I don't recommend quoting it. In most bacteria the difference was far less, but if I remember correctly, none that I looked at had all 100% identical 16S copies.

[SNPsaurus]

This is the ref that Brian was probably remembering:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057923

"The level of dissimilarity within a genome can be relatively high: fourteen genomes contained at least one pair of 16S rRNA sequences with a similarity below 97%"

However, most are more similar:
At a genome level, 19.8% of all genomes with more than one 16S rRNA copy harbor 2–5 identical 16S rRNA copies, and the average 16S rRNA similarity within a genome is 99.70±0.46%, with 97.6% of genomes showing average 16S rRNA similarity above 99%.

[bioinfobeginner]

This is the ref that Brian was probably remembering:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057923

"The level of dissimilarity within a genome can be relatively high: fourteen genomes contained at least one pair of 16S rRNA sequences with a similarity below 97%"

However, most are more similar:
At a genome level, 19.8% of all genomes with more than one 16S rRNA copy harbor 2–5 identical 16S rRNA copies, and the average 16S rRNA similarity within a genome is 99.70±0.46%, with 97.6% of genomes showing average 16S rRNA similarity above 99%.

Thanks SNPsaurus!

I appreciate your help.