The 2nd version of the Vitis labrusca genome annotation as released in 2024 from the Gschwend Grapevine Genetics Laboratory at The Ohio State University as first referenced in the manuscript 'Trichomes and Unique Gene Expression Confer Insect Herbivory Resistance in Vitis labrusca Grapevines' by Dixon & Gschwend. The accession employed for the creation of this gene annotation was Vitis labrusca acc. 'GREM4', the same accession used by the Gschwend Lab by Li & Gschwend 2023 (for the publication 'Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes') for the original annotation.
This folder contains all of the genes named as per their 'Data Analysis' nomenclature as well as their 'Finalized' nomenclature. The 'Data Analysis' nomenclature was used for all data analyses in the publication. These names were used for the data analysis because they were the names which were created by the gene annotation updating program (which was used to make version 2 of the genome for V. labrusca acc. 'GREM4'). Considering these names were generated by the program, we simply retained and used these names for downstream data analyses. Considering the complexity and less-than-ideal conventions inherent to these names, the 'Finalized' nomenclature was subsequently created and is the nomenclature that is found throughout the body, figures, and tables of the manuscript. Prior to July of 2024, this nomencluature was the system which we intended for all future studies pertaining to Vitis labrusca, and more specifically Vitis labrusca acc. 'GREM4', to use. Rest assured that the data found within each nomenclature system's folder is identical otherwise. Both nomenclature systems' data is provided herein, as, depending on the purpose of your exploration of the data, you may wish to know the gene names in one nomenclature system or the other as all supplemental materials are still in 'Data Analysis' nomenclature as conversion of all of the names in these files was not realisitic/feasible considering the time and effort this would take.
Importantly, as of July, 2024, the genome annotation was again updated to facilitate the uploading of the genome to the Vitis genome repository - grapegenomics.com. In this process, the naming of the genes was again changed, but again, rest assured, nothing materially changed with the genes, or any other associated content. We now ask that you use the genome annotation nomenclature and files available/as hosted on the grapegenomics website, the 'Grape Genomics Nomenclature', which can be found directly at https://www.grapegenomics.com/pages/VlaGREM4/ .
To aid in the conversion from 'Data Analysis Nomenclature' to 'Finalized Nomenclature' to 'Grape Genomics Nomenclature', the "Gene Nomenclature Conversion WkBk - Final V2" is provided which provides the gene name from all three systems to cross-reference against. Again, moving forward, we ask that all individuals use the 'Grape Genomics Nomenclature' to name genes to ensure consistency, and facilitate ease of comparison, between publications.
Additionally, the functional annotation can also be found as its own separate folder with data within pertaining to the functional annotation of the annotated genes.
File Type Descriptions:
For more explanation on the differences between UTRs, CDS's, pre-mRNA, mature mRNA, etc., please see below.
Gene Annotation (.gff3) File Description and Central Dogma Information:
