Annotation of non model fish (mahi mahi) genome

Question

[kspata]

Hi,

I have an assembled genome obtained from oxford nanopore reads. How can I perform a basic annotation to obtain a genbank file? What tools are available to perform eukaryotic genome annotation.

I had previously used RAST for bacterial genome annotations, can I use this tool for eukaryotic genoem annotation as well?

Thanks in advance !!

[GenoMax]

Take a look at MAKER. If you have a transcriptome available then: GAWN - Genome Annotation Without Nightmares

[Juke34]

Annotation of an assembly made on nanopore reads only can be very challenging. Good luck with that. Most annotation tools will not integrate conversion to Genbank or EMBL file, they will produce GFF or GTF file. You will probably have to perform this conversion yourself with GAG or EMBLmyGFF3.

If you want an exhaustive list of annotation tool, have a look here: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_genome.md

[Michael]

Afaik, you cannot use RAST because it doesn't support eukaryote gene models and uses only homology within bacteria as evidence.

[colindaven]

Have you polished the genome extensively (eg with medaka, racon?). Else your annotation will suffer from false frameshifts in reading frames due to indel errors. Even after polishing this is a big problem.

[COMB5014]

Hi Kspata, We are working on mahi-mahi research and looking for its genome information. The Google search led me to your post. We are looking for markers that can distinguish males from females and a gene called deadend. We hope to have the opportunity to work with you and are willing to reach an agreement with your team. Please contact our project lead Neil Sims [e-mail]. Many thanks.

Answer 1

[Shalu Jhanwar]

There are different genome annotation tools available. Have a looks at below resources to get the most comprehensive and widely accepted tools:

https://www.1010genome.com/eukaryotic-genome-annotation/

https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/

https://www.gensas.org/

[Michael]

I would also recommend gensas. You can also run BUSCO analysis there first. If you get low BUSCO completeness, this indicates that your genome needs more error correction. Also, you need some evidence data to derive gene models, like RNA-seq, ESTs, or protein data.