Hordeum vulgare transcripts addnotation

Question

[martta95]

Hello,

I have list of transcript mapped to Hordeum vulgare genome, e.g.,

HORVU.MOREX.r2.UnG0628590.1
HORVU.MOREX.r2.5HG0361000.1
HORVU.MOREX.r2.UnG0628880.1

I would like to add annotation about gene function and gene name, What tools I can use?

[GenoMax]

Please don't post same content in multiple threads. Prior thread for reference : Hordeum genes addnotation

[Ram]

I'm deleting the other thread as your answer here is more comprehensive than your comment there. But yes, martta95 - DO NOT open multiple threads for the same question. Next time, your duplicate posts will be deleted without warning.

Answer 1

[GenoMax]

Looks like your ID's are from a previous genome assembly.

A. Get the annotation file from Ensembl

wget https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-56/gff3/hordeum_vulgare_goldenpromise/Hordeum_vulgare_goldenpromise.GPv1.56.gff3.gz
gunzip Hordeum_vulgare_goldenpromise.GPv1.56.gff3.gz

B. Extract column 9 that contains information you want for only the transcript lines (mRNA)

awk -F "\t" '$3 ~ "mRNA" {print $3,$9}' Hordeum_vulgare_goldenpromise.GPv1.56.gff3 > Hordeum_col9 

C. Loop through your file if ID's (as shown above) to extract the relevant lines for transcript

for i in `cat id`; do grep -w "${i}" Hordeum_col9 ;done
mRNA ID=transcript:HORVU.MOREX.r2.UnG0628590.1.mrna1;Parent=gene:HORVU.MOREX.r2.UnG0628590.1;biotype=protein_coding;tag=Ensembl_canonical;transcript_id=HORVU.MOREX.r2.UnG0628590.1.mrna1
mRNA ID=transcript:HORVU.MOREX.r2.5HG0361000.1.mrna1;Parent=gene:HORVU.MOREX.r2.5HG0361000.1;biotype=protein_coding;tag=Ensembl_canonical;transcript_id=HORVU.MOREX.r2.5HG0361000.1.mrna1
mRNA ID=transcript:HORVU.MOREX.r2.UnG0628880.1.mrna1;Parent=gene:HORVU.MOREX.r2.UnG0628880.1;biotype=protein_coding;tag=Ensembl_canonical;transcript_id=HORVU.MOREX.r2.UnG0628880.1.mrna1
mRNA ID=transcript:HORVU.MOREX.r2.UnG0634500.1.mrna1;Parent=gene:HORVU.MOREX.r2.UnG0634500.1;biotype=protein_coding;tag=Ensembl_canonical;transcript_id=HORVU.MOREX.r2.UnG0634500.1.mrna1

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Since this does not get you much in terms of annotation you may want to try using BioMart at Gramene site: https://ensembl.gramene.org/biomart/martview