SEA-PHAGES | Should this gene be kept or deleted?

Link to this post \| posted 09 Nov, 2020 14:36
wasique	In Microbacterium phage PermaG, the data for gene 38 in PECAAN is quite confusing. It is an orpham with no BLAST or HHPred results. There is also no synteny. However, GeneMark shows some coding potential over the approx. 100 bp gene. This makes me confused about whether this gene should be deleted or whether it should be kept. In addition, we also considered whether this gene might be part of the previous or next gene. That isn't the case, however, since both the previous and next gene have synteny and distinct functions. Thank you in advance! 192Kb

Link to this post | posted 09 Nov, 2020 14:36

In Microbacterium phage PermaG, the data for gene 38 in PECAAN is quite confusing. It is an orpham with no BLAST or HHPred results. There is also no synteny. However, GeneMark shows some coding potential over the approx. 100 bp gene. This makes me confused about whether this gene should be deleted or whether it should be kept.
In addition, we also considered whether this gene might be part of the previous or next gene. That isn't the case, however, since both the previous and next gene have synteny and distinct functions.
Thank you in advance!

Link to this post \| posted 11 Nov, 2020 15:35
c.sunnen	Hi Wasique! Thanks for providing the entire annotation notebook entry! It's super helpful for making a call. While orphams are often not real, and you should definitely be skeptical, I would probably keep this gene exactly as you annotated it. First, it has really good coding potential (at least in the GM-self output). Second, it has a nice 1bp overlap with the previous gene (with the start you've chosen) and creates another 1bp overlap with the downstream gene; if you delete it, you create a big gap. These nice 1bp overlaps suggest an operon, and that all 3 genes (37, 38, 39) all get translated by the ribosome. Finally, it appears from your Phamerator screenshot that this specific area of the genome differs from closely related phages, as they have space for a gene (pham 7983, 6 members) that your genome does not; in fact, it looks like there may have been a deletion of some kind. So it's not surprising that you have a never-before-seen gene here; it's not like other phages in this cluster! Good job finding all the evidence. I think the evidence supports keeping it. Nikki Sunnen USciences PHAGES faculty SMART member

Link to this post | posted 11 Nov, 2020 15:35

c.sunnen

Hi Wasique!

Thanks for providing the entire annotation notebook entry! It's super helpful for making a call. While orphams are often not real, and you should definitely be skeptical, I would probably keep this gene exactly as you annotated it. First, it has really good coding potential (at least in the GM-self output). Second, it has a nice 1bp overlap with the previous gene (with the start you've chosen) and creates another 1bp overlap with the downstream gene; if you delete it, you create a big gap. These nice 1bp overlaps suggest an operon, and that all 3 genes (37, 38, 39) all get translated by the ribosome. Finally, it appears from your Phamerator screenshot that this specific area of the genome differs from closely related phages, as they have space for a gene (pham 7983, 6 members) that your genome does not; in fact, it looks like there may have been a deletion of some kind. So it's not surprising that you have a never-before-seen gene here; it's not like other phages in this cluster!

Good job finding all the evidence. I think the evidence supports keeping it.

Nikki Sunnen
USciences PHAGES faculty
SMART member

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Should this gene be kept or deleted?