Dear Biostars community,
I am working with the plants Ensembl database for the Barley (Morex v3) genome. While I have all the necessary files (Fa, GTF), I couldn't locate any details regarding the barley chloroplast and mitochondrial genomes.
- Although I found the Fasta file on NCBI GeneBank for Barley chloroplast genome I couldn't find a gene annotation file. Does such a file exist? Also, I'd prefer to have all genomes from the same database and Ensembl preferred by some tools I am using.
- Additionally, is there any information available about the coordinates of repetitive regions?
thank you
1 answer
To find mitochondrial genome sequences and annotations, you can go to https://www.ncbi.nlm.nih.gov , select "Nucleotide" to the left of the search field and search for
"Hordeum vulgare" [organism] AND "mitochondrion" [title] AND "complete" [title]
You'll find a lot of assembled and annotated mitochondrial genomes of different samples of the barley.
The same you can do for the chloroplast genome, just replace "mitochondrion" with "chloroplast".
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RefSeq assembly for Morex v3 genome is supposed to contain chloroplast sequence: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/904/849/725/GCF_904849725.1_MorexV3_pseudomolecules_assembly/. You will also find genome annotation files there.
Based on stats from the main genome page; https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_904849725.1/
In case it helps, the previous barley version at Ensembl Plants did contain organellar genomes, you can browse them at https://nov2020-plants.ensembl.org/Hordeum_vulgare/Info/Index?db=core
An example cp region can be see here: https://nov2020-plants.ensembl.org/Hordeum_vulgare/Location/View?db=core;r=Pt:7987-107987
Sometimes getting the required information is very difficult