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Tribolium castaneum
Summary
| Type |
organism
|
|---|---|
| Genus |
Tribolium
|
| Species |
castaneum
|
| Common Name |
Red flour beetle
|
| Description | |
| Publication |
|
| Organism Image |
|
| Image Credit |
Copyright Susan J. Brown
|
Assembly Stats
| Contig N50 |
16.2 Mb
|
|---|---|
| GC Content |
31.5
|
| Scaffold N50 |
20.6 Mb
|
Other Information
| Community Contact |
Erin Scully, USDA-ARS
|
|---|---|
| Links |
Analyses
| Name | Program |
|---|---|
| Tribolium castaneum annotations TCAS_OGSv3 | AUGUSTUS |
| Functional annotation of Tribolium castaneum annotations TCAS_OGSv3 | AgBase functional annotation pipeline |
| Tribolium castaneum genome assembly Tcas5.2 (GCF_000002335.3) | AllPaths v. 2008; ATLAS-LINK v. 2014; GapFiller v. 2014; stitch v. 2014 |
| NCBI Tribolium castaneum Annotation Release 103 | NCBI Eukaryotic Genome Annotation Pipeline |
| Tribolium castaneum genome assembly icTriCast1.1 (GCF_031307605.1) | HiFiASM |
| NCBI Tribolium castaneum Annotation Release GCF_031307605.1-RS_2024_04 | NCBI Eukaryotic Genome Annotation Pipeline |
| Functional annotation of NCBI Tribolium castaneum Annotation Release GCF_031307605.1-RS_2024_04 | AgBase functional annotation pipeline |
| Tribolium castaneum annotations TCAS_OGSv3.1 | LiftOff |
| Functional annotation of Tribolium castaneum annotations TCAS_OGSv3.1 | AgBase functional annotation pipeline |
Tribolium castaneum, the red flour beetle, is a secondary pest of stored grain. It has emerged as a premier genetic model organism for studies of development and pest management. A robust RNAi response at any life stage has enabled functional studies of all live stages covering processes from development to physiology. In terms of genetic and transgenic tools including genome wide RNAi screening, T. castaneum is an insect model second only to D. melanogaster.
T. castaneum is a cosmopolitan pest of wheat that is easily reared in the laboratory on a diet of whole wheat flour supplemented with 5% yeast. At 29C, T. castaneum completes embryonic development in 3 days and generally undergoes 6 larval molts before metamorphosis into adults. Although the life cycle can be completed within 3 weeks, adults can live for a year while females reproduce for several months.
The T. castaneum genome contains 10 autosomes, an X and a Y. The genome is 200Mb, 160 of which have been captured in the latest genome assembly, Tcas_5.2. The original 7x Sanger draft was improved with additional NGS data and 90% of the assembled sequence has been mapped to Linkage Groups. Scaffolds in the resulting CHLG builds have been merged ordered and oriented using optical maps.
Genome update. Previously, the i5k Workspace@NAL hosted Tribolium castaneum genome assembly Tcas5.2 (GCF_000002335.3), NCBI Tribolium castaneum Annotation Release 103, Tribolium castaneum annotations TCAS_OGSv3 and Functional annotation of Tribolium castaneum annotations TCAS_OGSv3. The assembly and annotations have updated to the most recent assembly, Tribolium castaneum genome assembly icTriCast1.1 (GCF_031307605.1), Tribolium castaneum annotations TCAS_OGSv3.1, NCBI Tribolium castaneum Annotation Release GCF_031307605.1-RS_2024_04 and Functional annotation of NCBI Tribolium castaneum Annotation Release GCF_031307605.1-RS_2024_04.
This genome update is part of the Ag100Pest project (http://i5k.github.io/ag100pest).