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Whole transcriptome annotation files

Version 4 2023-02-27, 20:46
Version 3 2022-07-26, 20:06
Version 2 2022-04-06, 18:39
Version 1 2022-01-08, 02:49
posted on 2023-02-27, 20:46 authored by David Stern, Clair HanClair Han

These are the manually corrected BRAKER annotations in GFF3 format, from Table S5 of "Gene Structure-Based Homology Search Identifies Highly Divergent Putative Effector Gene Family", Stern and Han, https://doi.org/10.1093/gbe/evac069

Please contact Clair Han at hanc@janelia.hhmi.org with any questions.

See related materials in collection at: https://doi.org/10.25378/janelia.c.5778905.


Hormaphis cornus GFF (7/26/22):

-The manuscript lists Augustus.updated_w_annots.19viii21_final.gff3 as the GFF used. The correct version should be Augustus.updated_w_annots.3ix21_final.gff3. There are very few changes between these version.

-This GFF has since then been further updated to Augustus.updated_w_annots.1vii22_final.gff3.

Both Augustus.updated_w_annots.3ix21_final.gff3 and Augustus.updated_w_annots.1vii22_final.gff3 are provided. 

Tetraneura nigriabdominalis GFF (2/25/23):

-The manuscript uses Tnig.Augustus.updated_w_annots.7vii21.gff3.

-However, the compatible GFF to be used with our genome on Genbank (accession JAIUCT000000000) is Tnig.Augustus.updated_w_annots.7vii21_genbank_final.gff3. The discrepancy is due to changes in the reference genome contig names in the Genbank upload. Both GFFs are provided. 

-Alternatively, the manuscript GFF could be used with the Genbank reference genome using the contig names conversion table available on Genbank: https://www.ncbi.nlm.nih.gov/Traces/wgs/JAIUCT01?display=contigs