SEA-PHAGES | Is this a sequencing error?

Link to this post \| posted 14 Jul, 2021 19:40
MSMC	We are annotating genes 8 and 9 in Looper (A15). These two genes are currently orphams. When we look at the same region in similar phages, it's highly conserved and called as one gene (Pham 69334 - 723 members of the pham). When the region from Looper is BLASTed, the alignment shows one nucleotide difference compared to similar phages (see attached), and this results in a stop codon - therefore 2 genes in Looper and one gene in the other phages. There is little coding potential for the second gene in Looper (both programs call it a gene), but the coding potential is minimal for the second half of the gene in similar phages. So the question is, is this a sequencing error? It seems unlikely that one phage out of hundreds would have a mutation leading to a stop codon resulting in two functional genes. Edited 14 Jul, 2021 19:47 78Kb

Link to this post | posted 14 Jul, 2021 19:40

We are annotating genes 8 and 9 in Looper (A15). These two genes are currently orphams. When we look at the same region in similar phages, it's highly conserved and called as one gene (Pham 69334 - 723 members of the pham). When the region from Looper is BLASTed, the alignment shows one nucleotide difference compared to similar phages (see attached), and this results in a stop codon - therefore 2 genes in Looper and one gene in the other phages. There is little coding potential for the second gene in Looper (both programs call it a gene), but the coding potential is minimal for the second half of the gene in similar phages.

So the question is, is this a sequencing error? It seems unlikely that one phage out of hundreds would have a mutation leading to a stop codon resulting in two functional genes.

Edited 14 Jul, 2021 19:47

Link to this post \| posted 15 Jul, 2021 14:25
DanRussell	Hey Evan, You make a good case as to why this one merits a check as a potential sequencing error, and it has some of those red flags (different from similar genomes, breaks a gene). But I just checked the sequencing data and see this: The base in question is a couple to the right of the green line, and the "A" called there is really strongly supported with no conflicting reads. So it's a real biological thing! –Dan

Link to this post | posted 15 Jul, 2021 14:25

DanRussell

Hey Evan,

You make a good case as to why this one merits a check as a potential sequencing error, and it has some of those red flags (different from similar genomes, breaks a gene). But I just checked the sequencing data and see this:

The base in question is a couple to the right of the green line, and the "A" called there is really strongly supported with no conflicting reads. So it's a real biological thing!

–Dan

Link to this post \| posted 15 Jul, 2021 14:32
MSMC	DanRussell Hey Evan, You make a good case as to why this one merits a check as a potential sequencing error, and it has some of those red flags (different from similar genomes, breaks a gene). But I just checked the sequencing data and see this: The base in question is a couple to the right of the green line, and the "A" called there is really strongly supported with no conflicting reads. So it's a real biological thing! –Dan Great, thanks so much for checking this Dan!

Link to this post | posted 15 Jul, 2021 14:32

MSMC

DanRussell
Hey Evan,

You make a good case as to why this one merits a check as a potential sequencing error, and it has some of those red flags (different from similar genomes, breaks a gene). But I just checked the sequencing data and see this:

The base in question is a couple to the right of the green line, and the "A" called there is really strongly supported with no conflicting reads. So it's a real biological thing!

–Dan

Great, thanks so much for checking this Dan!

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Is this a sequencing error?