Link to this post | posted 02 May, 2024 21:23

c.sunnen

Hi! We are annotating PhesterPhotato, an F1 cluster phage, and it's got some extra weirdness, even for an F1! Please see the attached Phamerator + Genemark output picture. There's a forward gene (47) in the middle of a small group of reverse genes. It overlaps. But there may be a reverse gene instead (46). There's evidence for both, though better CP for the forward (47) than the reverse. Some other F1s call the forward (12 total members in pham), some call the reverse gene (again, 12 total members). If I call the reverse, in order to capture the CP, I'd have to create an overlap with gene #48, which no one does, so I'm feeling like this tiny reverse gene isn't real. But why would there be a forward in the middle of these reverse? Creating an overlap? Most other phages don't call either, and just leave a big (300bp) gap. Please help. It's in PECAAN if you want to look at it there. No evidence for function for either 46 or 47, but 48 is likely the immunity repressor. Thanks! Nikki & the SJU team 1.89Mb

Link to this post | posted 03 May, 2024 16:20
debbie	Hi Nikki, Mycobacteriophage Tweety has a paper that includes mass spec data. While the integrase and repressor have less sequence homology, that space in between may have enough similarity that you can draw some inferences that are applicable. Let me know what you think. https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13946 Best, debbie Edited 03 May, 2024 16:22

Link to this post | posted 03 May, 2024 17:55

c.sunnen

The paper you linked has a nice RNAseq map of Fruitloop in Figure 4, in addition to the mass spec data in Table 1. Yes, that's very helpful! Fruitloop does have 95% sequence similarity in this region to PhesterPhotato, and Fruitloop doesn't call either of these genes (46 and 47 in PhesterPhotato). When I look at GM-S coding potential from Fruitloop in this area, there is a little CP in the forward direction in the gap between 43 and 44 (between 45 and 48 in PhesterPhotato), but it's only atypical, and not as strong as it is in PhesterPhotato. The RNA seq from Fruitloop makes it look like MAYBE there's a reverse gene in there that gets expressed during lysogeny, but it's hard to see, and definitely there's not a forward gene expressed. The mass spec doesn't show these genes being made (nor the flanking reverse genes, either though, including the immunity repressor), but I guess that's still evidence that neither of these is real. I'll delete both 46 and 47 from PhesterPhotato, so that it matches with Fruitloop. Thank-you!

Link to this post | posted 03 May, 2024 17:55

c.sunnen

The paper you linked has a nice RNAseq map of Fruitloop in Figure 4, in addition to the mass spec data in Table 1. Yes, that's very helpful! Fruitloop does have 95% sequence similarity in this region to PhesterPhotato, and Fruitloop doesn't call either of these genes (46 and 47 in PhesterPhotato). When I look at GM-S coding potential from Fruitloop in this area, there is a little CP in the forward direction in the gap between 43 and 44 (between 45 and 48 in PhesterPhotato), but it's only atypical, and not as strong as it is in PhesterPhotato. The RNA seq from Fruitloop makes it look like MAYBE there's a reverse gene in there that gets expressed during lysogeny, but it's hard to see, and definitely there's not a forward gene expressed. The mass spec doesn't show these genes being made (nor the flanking reverse genes, either though, including the immunity repressor), but I guess that's still evidence that neither of these is real. I'll delete both 46 and 47 from PhesterPhotato, so that it matches with Fruitloop. Thank-you!

Link to this post | posted 03 May, 2024 18:42
debbie	Be careful what you say about Fruitloop. Go to the paper and see the mas spec table and the map there. (when I looked, the paper doesn't match the GB file). There is a gene in there that you do want to call. i just don't have time right now to match it correctly. Let's touch base before you submit. best, debbie

Link to this post | posted 04 May, 2024 13:29
c.sunnen	Thanks, Debbie. Will check back in later, before we send it in.

Link to this post | posted 09 May, 2024 02:16
debbie	Hi Nikki, Sorry to id the paper as Tweety, when the data is about Fruitloop. Bit I di have the paper right! (Just what you needed, more confusion.) I think your decision is a good as we can get at this point. best, debbie