Research Resources
IWGSC Chinese Spring Reference genome gene annotation conversion table (created by Fernando Correr)
We connected the wheat gene identifiers using the annotation files from version 1.1 to 2.1. The files used were the two GFF3 files from v1.1 and v1.2, and a mapping file between v2.1 and v1.2:
- IWGSC_v1.1_HC_20170706.gff3: Download the file https://urgi.versailles.inrae.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.1/iwgsc_refseqv1.1_genes_2017July06.zip
- IWGSC_v1.2_HC_20200615.gff3: Download the file https://urgi.versailles.inrae.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.2/iwgsc_refseq_v1.2_gene_annotation.zip
- iwgsc_refseqv2.1_annotation_200916_IDmapping.csv: Download the file https://urgi.versailles.inrae.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v2.1/iwgsc_refseqv2.1_gene_annotation_200916.zip
For v1.1 we simply processed the identifier of the high confidence (HC) genes, selected along with the information of chromosomes, positions of start and end of the gene, and strand. Similarly, we followed the same procedure with v1.2, but also extracted previous identifiers and kept the descriptions of this version. For the v1.2 and v2.1 identifiers, we kept the mapping of HC genes that was provided in the IWGSC website (for v2.1 version). To join v1.1 and v1.2, we respectively used the gene identifier and the previous identifier. Then, we mapped the v1.2 identifier from the previous joining and the mapping file (v1.2 and v2.1). The final table has the following structure:
|
Column |
Description |
|
Chr_v1.2 |
Chromosome in version v1.2 |
|
Start_v1.2 |
Start position of gene in version v1.2 |
|
End_v1.2 |
End position of gene in version v1.2 |
|
Type_v1.2 |
Type of gene – curated or non-curated v1.2 |
|
Strand_v1.2 |
Strand of the gene in version v1.2 |
|
GFF_desc_v1.2 |
Description of v1.2 GFF |
|
ID_v1.2 |
Gene identifier in v1.2 |
|
Previous_v1.2 |
Previous gene identifier that is described in v1.2. This field corresponds to gene identifiers in v1.1 (can be also read as ID_v1.1) |
|
Chr_v1.1 |
Chromosome in version v1.1 |
|
Start_v1.1 |
Start position of gene in version v1.1 |
|
End_v1.1 |
End position of gene in version v1.1 |
|
Type_v1.1 |
Type of gene – curated or non-curated v1.1 |
|
Strand_v1.1 |
Strand of the gene in version v1.1 |
|
new_ID_v2.1 |
Gene identifier from v2.1 |
Please alert us if any errors are discovered.