ValWood
commented
2 months ago We should chat about this. We needed to remove the old "Lang" mitochondrial genome from the "ENA project" because we are not the official 'owners/authority'.
We did not replace by Li-Lin's version (the corrected version we are using in PomBase) because we are not the 'owners/authority' for this sequence.
The version we represent in PomBase is: AC MK618072; XX PR Project:PRJNA525552;
Also, be wary of using the submission, there is some mix-up with the db_xrefs ENA is trying to resolve.
Hello @kimrutherford and @ValWood, first congrats on managing to pass the submission pipeline!
I noticed that the new submission no longer includes the mitochondrial chromosome sequence. I know that this is because we moved from NC_001326.1 to MK618072.1.
However, this can be a bit problematic (at least for me). Before, using the NCBI datasets API, you could access the sequences and annotation of mitochondrial genes, but now you can't find them. I wonder if there is a way to include it as part of the assembly? Also, this means that our latest updated mitochondrial annotation cannot be found anywhere on NCBI.
before: https://www.ncbi.nlm.nih.gov/datasets/gene/GCF_000002945.1/?search=cox2 after: https://www.ncbi.nlm.nih.gov/datasets/gene/GCA_000002945.3/?search=cox2
Tagging @olearyna in case she has some advice.