SEA-PHAGES | 90 bp overlap between forward and reverse genes

Link to this post \| posted 13 Mar, 2017 20:30
akoga	We are working on our genome called asapag, which is one of a few founding members of Cluster DN (Gordonia phage). We have just gotten to an area that I’m struggling with. Glimmer calls two little forward genes, one of which is also called by GeneMark. They are Genes 36 (28776-28910) and 37 (28975-29097). The next gene called is a reverse gene. There is not much coding potential for Genes 36 and 37, but there is great coding potential in that area in the reverse direction (even though neither glimmer or GeneMark call a reverse gene here). I tried creating a reverse gene (29588-28416) and I get a great Blast hit to gp 30 from Schwabeltier. However, creating this gene would cause a 90 bp overlap with the previous forward gene and has a poor SD score. In looking at Schwabeltier gp 30, it looks as though it also has a 90 bp overlap with its previous gene 29. One other note: 2 other drafts, Horus and Getalong have the first gene also (100% identical) and Getalong also has the second gene at 100% identical. It seems like I should delete the two forward genes and replace with the reverse gene, but is a 90 bp overlap too crazy?

Link to this post | posted 13 Mar, 2017 20:30

We are working on our genome called asapag, which is one of a few founding members of Cluster DN (Gordonia phage). We have just gotten to an area that I’m struggling with. Glimmer calls two little forward genes, one of which is also called by GeneMark. They are Genes 36 (28776-28910) and 37 (28975-29097). The next gene called is a reverse gene. There is not much coding potential for Genes 36 and 37, but there is great coding potential in that area in the reverse direction (even though neither glimmer or GeneMark call a reverse gene here). I tried creating a reverse gene (29588-28416) and I get a great Blast hit to gp 30 from Schwabeltier. However, creating this gene would cause a 90 bp overlap with the previous forward gene and has a poor SD score. In looking at Schwabeltier gp 30, it looks as though it also has a 90 bp overlap with its previous gene 29. One other note: 2 other drafts, Horus and Getalong have the first gene also (100% identical) and Getalong also has the second gene at 100% identical. It seems like I should delete the two forward genes and replace with the reverse gene, but is a 90 bp overlap too crazy?

Link to this post \| posted 26 Mar, 2017 17:39
debbie	Ann, Sorry for the delay in this response. I am not speaking specifically and to do this properly, i would need the file and supporting materials to truly evaluate. BUT in this case, I would say it is absolutely correct to look at the reverse frame for possible better calls. You may need to go back to Schwabeltier and check out the evidence for calling that gene (simplest to run GeneMark, I think), because you don't want to perpetuate a call that had no evidence in the first place. When you blast this reverse gene at NCBI - does it hit anything outside of our genomes? That would also validate it a bit. What does HHPRed say? Though we don't see it often, it is acceptable for the C' end of a forward and reverse gene to overlap. I just called one in Arthrobacter phage Jasmine (genes 32 & 33) with a whopping overlap. Note that all the genomes in Cluster DN are drafts, so none have been evaluated. You might want to communicate with the others and work on the difficult ones collaboratively. Remember to include this difficult stuff in your cover letter to SMART. Keep up the good work!

Link to this post | posted 26 Mar, 2017 17:39

debbie

Ann,
Sorry for the delay in this response. I am not speaking specifically and to do this properly, i would need the file and supporting materials to truly evaluate. BUT in this case, I would say it is absolutely correct to look at the reverse frame for possible better calls. You may need to go back to Schwabeltier and check out the evidence for calling that gene (simplest to run GeneMark, I think), because you don't want to perpetuate a call that had no evidence in the first place. When you blast this reverse gene at NCBI - does it hit anything outside of our genomes? That would also validate it a bit. What does HHPRed say?
Though we don't see it often, it is acceptable for the C' end of a forward and reverse gene to overlap. I just called one in Arthrobacter phage Jasmine (genes 32 & 33) with a whopping overlap.
Note that all the genomes in Cluster DN are drafts, so none have been evaluated. You might want to communicate with the others and work on the difficult ones collaboratively. Remember to include this difficult stuff in your cover letter to SMART. Keep up the good work!

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90 bp overlap between forward and reverse genes