Is there any update about adding more reference genomes of plant species on Ensemble?

Question

[biotechnology415]

I have been trying snp annotation on ensemble. But as far as I tried and observed, it has reference genomes of only few species of a particular crop. In my case, I am trying to annotate snps of Gossypium hirsutum , but when I searched on the database, only reference sequences of Gossypium raimondii is available. As Gossypium hirsutum is the most widely cultivated among all species of cotton, and in the past decade, extensive sequencing programs have been successfully accomplished, generating a huge amount of genome information. Integrating G.hirustum genome sequences on ensemble database would be very helpful for exploring its genome. Or may be, it is already integrated in the database, and i am unable to access it. Can anyone make it clear? Is it integrated in the database ? Is there any future plan to integrate more plant species?

[biotechnology415]

Thank you so much for your quick response.

[Ram]

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Answer 1

[Emily]

We have it on our list of genomes to add but we're waiting for the latest 2020 version to be given a GCA accession by the INSDC, as this is a requirement for us.

If you want to annotate your variants, you can still do so using the Ensembl VEP. If you can get a genome FASTA file and matching gene annotation in GTF or GFF, you can run the VEP with custom data.