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i5k Workspace@NAL
U.S. Department of Agriculture
  1. Genomeannotation
  2. Tribolium Castaneum Annotations TCAS_OGSv3.1

Tribolium castaneum annotations TCAS_OGSv3.1

Summary
Type
Genome annotation
Name
Tribolium castaneum annotations TCAS_OGSv3.1
Description

The original Tribolium castaneum annotations TCAS_OGSv3 gff3 file (https://i5k.nal.usda.gov/data/Arthropoda/tricas-%28Tribolium_castaneum%29/GCF_000002335.3/2.Official%20or%20Primary%20Gene%20Set/TCAS_OGS_v3/GCA_000002335.3_Tcas5.2_genomic_RefSeqIDs.gff) was lifted over to assembly icTriCast1.1 (GCF_031307605.1) using the software LiftOff v1.6.3 (https://github.com/agshumate/Liftoff), using the -exclude_partial and -polish options. 188 gene models were not lifted over. A list of their identifiers can be found in https://i5k.nal.usda.gov/data/Arthropoda/tricas-%28Tribolium_castaneum%29/icTriCast1.1/2.Official%20or%20Primary%20Gene%20Set/TCAS_OGS_v3.1/unmapped_features.txt. 73.3% of the lifted models are unchanged; 97.6% of the lifted models have 95% or higher sequence identity at the nucleotide level with the original model. LiftOff statistics for individual models are available in https://i5k.nal.usda.gov/data/Arthropoda/tricas-%28Tribolium_castaneum%29/icTriCast1.1/2.Official%20or%20Primary%20Gene%20Set/TCAS_OGS_v3.1/tricas_OGSv3.1_liftoff_stats.txt. For more information about LiftOff, see https://github.com/agshumate/Liftoff

LiftOff command: liftoff -g GCA_000002335.3_Tcas5.2_genomic_RefSeqIDs.gff -o GCA_000002335.3_Tcas5.2_genomic_RefSeqIDs-lifted.gff -exclude_partial -polish GCF_031307605.1_icTriCast1.1_genomic.fna GCF_000002335.3_Tcas5.2_genomic_RefSeqIDs.fna

The lifted models were functionally annotated with the AgBase functional annotation pipeline. Gene Ontology (GO) annotations are derived from agbase/goanna:2.2 (https://hub.docker.com/repository/docker/agbase/goanna) with ECO:0000247 or from agbase/interproscan:5.45-80 (https://hub.docker.com/repository/docker/agbase/interproscan) with ECO:0000501. Pathway annotations are derived from agbase/kobas:3.0.3_0 (https://hub.docker.com/repository/docker/agbase/kobas) with ECO:0000247.
Program, Pipeline, Workflow or Method Name
LiftOff
Program Version
1.6.3
Source Name
Tribolium castaneum genome assembly icTriCast1.1 (GCF_031307605.1)
Data Source URI

https://i5k.nal.usda.gov/data/Arthropoda/tricas-%28Tribolium_castaneum%…
Organism
Tribolium castaneum
Publication
Herndon N, Shelton J, Gerischer L, Ioannidis P, Ninova M, Dönitz J, Waterhouse RM, Liang C, Damm C, Siemanowski J, Kitzmann P, Ulrich J, Dippel S, Oberhofer G, Hu Y, Schwirz J, Schacht M, Lehmann S, Montino A, Posnien N, Gurska D, Horn T, Seibert J, Vargas Jentzsch IM, Panfilio KA, Li J, Wimmer EA, Stappert D, Roth S, Schröder R, Park Y, Schoppmeier M, Chung HR, Klingler M, Kittelmann S, Friedrich M, Chen R, Altincicek B, Vilcinskas A, Zdobnov E, Griffiths-Jones S, Ronshaugen M, Stanke M, Brown SJ, Bucher G. Enhanced genome assembly and a new official gene set for Tribolium castaneum.. BMC genomics. 2020 Jan 14; 21(1):47.