I have helped a lab sequence a mitochondrial genome. I used then MITOS to annotate the genome (warning them that I did it just for curiosity as I am not experienced). They submitted the sequence and annotation to genbank but it was refused for different reasons.
It's the genome of a species for which there is no reference. It's a jumping spider and the genome is almost identical to the one below. I used MITOS web server and I got an annotation almost identical to this one (http://mitos.bioinf.uni-leipzig.de/result.py?hash=bJuyJw4b) which corresponds to this sequence (https://www.ncbi.nlm.nih.gov/nuccore/MH891570 ). But the submitted annotation to Genbank is slightly different so I guess they manually edited it or they used another software. I am not sure I can share more specific information without the permission of the lab.
You can download a GFF file or the raw sequence at the page in the link (for the similar sequence).
My questions are as follows:
- after applying MITOS, is there any manual or automatic review that should be applied?
- Is it common that the annotation returned by MITOS is not good enough?
- Or could that indicate that maybe there is a problem in the assembled genome? (looks unlikely except for a few SNPs as three assemblers return almost the same sequence)
- Should we edit the annotation ourselves or there is a software that does it itself?
- How often using MITOS is enough or how often manually editing is needed?
The sequence corresponds to an arachnid. The reasons given by Genbank are:
Some or all of the sequences contain incorrect annotation and/or contain little similarity to other sequences in the database based on BLAST searches. Please also review your nucleotide sequences for issues such as low quality data or frameshifts.
Incorrect annotation is:
- coding regions lack stop codons
- CDS features do not have the correct nucleotide spans or location for example, nad5 is longer at the amino terminus compared to similar proteins in the database and extends into the flanking tRNA.
The first part of their reply is apparently generic as I have seen the same answer in another submission in which I didn't participate. I am not sure it's even verified as there are quite good BLAST matches. I have no idea about the other part. I just applied MITOS.
I used the invertebrate mitochondrial translation table option in MITOS. I guess it's the correct one as the result quite makes sense except for small adjustments.