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duplicated genes at start/end of genome

| posted 05 Apr, 2022 21:59
We are annotating the two FM cluster phages, Ottawa and Kharcho which both have two duplicated genes at the start (1 and 2) and end (105 and 106) of the phage. They are identical in protein sequence(head-to-tail stopper, minor capsid protein), so even though the h-t stopper can appear only once we will annotate both with the same functions. Is this architecture common? I assume there was a recombination event that might have happened during circularization or excision? Can someone point us to other phages that have the same architecture?
| posted 06 Apr, 2022 16:14
Hi. Genome organization is something that is worked out during the sequencing of phages. We are keen to make sure we have been precise with the ends of our phage genomes. The type of ends fall into 3 categories:
    Those with cos ends, meaning there is an overhang of sequence, usually about 10 bases long this 'sticks the genome together Those with no ends - because these phages use a head-full-packaging mechanism that puts in > the genome length, but the start/stop of that length is not the same in every genome Those with direct terminal repeats, meaning that that genome when it circularizes in the host will overlap for the length of the repeat - so even though you see identical genes at the front and back of a genome (and you SHOULD see identical genes because the sequence is identical) there will only be one copy of them in the working phage genome.
The phage page is chocked full of information about the phage, check there to see how Ottawa and Kharcho's genomes are described!
Edited 06 Apr, 2022 16:21
| posted 06 Apr, 2022 16:19
thanks Debbie! I think you meant to link to a page - I assume it is in the Bioinformatics guide, and I should have looked there first…
| posted 06 Apr, 2022 16:25
No, I meant the phage pages, they describe the specific ends type of the phage genome. I am trying to remember a good resource that gives the biology behind this, but I am still thinking about that. Although, there will be some good info concerning this in one of Dan's videos.

| posted 06 Apr, 2022 16:35
OK, I understand. He did talk about this in his faculty meeting talk, and Erika ran some of the end programs…I will check with her about she found. So this is common, and they should be identical.

For the annotation, I assume we still submit those last two genes.
| posted 06 Apr, 2022 16:44
Yes please! They should be identical to whatever is the beginning of the genome.
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