SEA-PHAGES | Potential feature deletion in Ibouu (cluster F)

Link to this post \| posted 22 Sep, 2025 16:46
allie.c.smith@ttu.edu	We are currently annotating Ibouu, which is in cluster F I have a specific question about Feature 42 which is a reverse at bp position 31492bp-31434bp This feature overlaps it's upstream feature 41 (which is a forward) by nearly half its bp. length at position 31218bp-31379bp, and feature 42 is not identified by GeneMark with little coding potential. Features 41 (31218bp-31379bp) and 43 (31738bp-31544bp) which is also a Reverse have high coding potential per GenMark and we feel are real genes which we plan to leave included in the annotation. I was hoping to get guidance on deleting Feature 42 - even though it would leave a gap between features 41 and 43, we feel that because it overlaps so much with the previous gene and it has weak coding potential and wasn't auto-annotated by GeneMark at all, it should be deleted from our annotation. Please let me know what you think. Thanks,

Link to this post | posted 22 Sep, 2025 16:46

allie.c.smith@ttu.edu

We are currently annotating Ibouu, which is in cluster F

I have a specific question about Feature 42 which is a reverse at bp position 31492bp-31434bp

This feature overlaps it's upstream feature 41 (which is a forward) by nearly half its bp. length at position 31218bp-31379bp, and feature 42 is not identified by GeneMark with little coding potential.

Features 41 (31218bp-31379bp) and 43 (31738bp-31544bp) which is also a Reverse have high coding potential per GenMark and we feel are real genes which we plan to leave included in the annotation.

I was hoping to get guidance on deleting Feature 42 - even though it would leave a gap between features 41 and 43, we feel that because it overlaps so much with the previous gene and it has weak coding potential and wasn't auto-annotated by GeneMark at all, it should be deleted from our annotation.

Please let me know what you think.
Thanks,

Link to this post \| posted 22 Sep, 2025 17:13
debbie	Hi Allie, I would keep it. I particularly like the coding potential (those slight) when using M. tb as the model. I am also not as concerned about the overlap, because it is the c-terminus of both genes that overlap, meaning that as they get transcribed/translated, the process started upstream and went through to completion. there is no upstream sequence needed to get their translation/transcription started. Note too, that the sequence is well-conserved across other clusters, even though these are tiny little genes. What do you think? debbie

Link to this post | posted 22 Sep, 2025 17:13

debbie

Hi Allie,
I would keep it. I particularly like the coding potential (those slight) when using M. tb as the model.
I am also not as concerned about the overlap, because it is the c-terminus of both genes that overlap, meaning that as they get transcribed/translated, the process started upstream and went through to completion. there is no upstream sequence needed to get their translation/transcription started.

Note too, that the sequence is well-conserved across other clusters, even though these are tiny little genes.

What do you think?
debbie

Link to this post \| posted 24 Sep, 2025 17:39
allie.c.smith@ttu.edu	Thanks so much for the feedback! We will plan to keep Feature 42 in the annotation. We came across one additional Feature that may be a candidate for deletion - Also in Ibouu, there is a stretch of forward genes at Feature 89 (50477-50701bp) and Feature 91 (50689-50862bp) that are almost contiguous and seem like great gene candidates. However, Feature 90R (50695-50546bp) is a reverse, and orpham, and completely overlaps with Feature 89. In our opinion, it should be deleted. What do you think? Thanks!

Link to this post | posted 24 Sep, 2025 17:39

allie.c.smith@ttu.edu

Thanks so much for the feedback! We will plan to keep Feature 42 in the annotation.

We came across one additional Feature that may be a candidate for deletion -

Also in Ibouu, there is a stretch of forward genes at Feature 89 (50477-50701bp) and Feature 91 (50689-50862bp) that are almost contiguous and seem like great gene candidates. However, Feature 90R (50695-50546bp) is a reverse, and orpham, and completely overlaps with Feature 89. In our opinion, it should be deleted.
What do you think?

Thanks!

Link to this post \| posted 24 Sep, 2025 18:59
debbie	Hi Allie, Yes, i think that Feature 89 (50477-50701bp) and Feature 91 (50689-50862bp) have more evidence to support keeping them than Feature 90R (50695-50546bp). I would delete Feature 90R (50695-50546bp). Best, debbie

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Potential feature deletion in Ibouu (cluster F)