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Functional annotation for 15 diverse arthropod genomes

The general approach for functional annotation is to combine GO annotations transferred on the basis of sequence homology (e.g., BLAST) with information about functional motifs (e.g., derived from resources such as PFAM). Gene products are mapped to metabolic and signalling pathways based upon sequence homology or orthology.

We present the annotation results of 15 arthropod proteomes using an open source, open access and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to a diverse range of arthropod species. You can find more information about the pipeline at our readthedocs site. The files for each genome include GOanna, InterproScan and KOBAS predictions.

Arthropod genomes selected for this study and their assembly and annotation statistics.

  1. Apis Mellifera (honey bee)
  2. Drosophila melanogaster (fruit fly)
  3. Tribolium castaneum (red flour beetle)
  4. Latrodectus hesperus (Western black widow spider)
  5. Limnephilus lunatus (caddisfly)
  6. Oncopeltus fasciatus (Large milkweed bug)
  7. Homalodisca vitripennis (Glassy-winged sharpshooter)
  8. Eurytemora affinis (calanoid copepod)
  9. Agrilus planipennis (emerald ash borer)
  10. Copidosoma floridanum (parasitoid wasp)
  11. Athalia rosae (turnip sawfly)
  12. Ceratitis capitata (Mediterranean fruit fly)
  13. Cimex lectularius (Cimicidae bed bug)
  14. Varroa destructor(parasitic mite)
  15. Diaphorina citri (Asian citrus psyllid)
See all >>
FieldValue
Tags
gene annotation
Gene ontology
Pathways
functional annotation
Modified
2022-09-22
Release Date
2021-07-07
Identifier
7a6a05b8-8652-4a93-b05d-38f13e239952
Spatial / Geographical Coverage Area
POLYGON ((-125.33203125 30.654452824401, -125.33203125 48.848450835898, -74.35546875 48.848450835898, -74.35546875 30.654452824401))
Publisher
Ag Data Commons
Temporal Coverage
July 6, 2021
License
Creative Commons CCZero
Contact Name
Saha, Surya
Contact Email
ss2489@cornell.edu
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Saha, Surya (ORCID)
Cooksey, Amanda M. (ORCID)
Childers, Anna K. (ORCID)
Poelchau, Monica F. (ORCID)
McCarthy, Fiona M. (ORCID)
Peer Reviewed
No
Intended Use
This functional annotation data provides a broad coverage of gene ontology (GO) terms and pathways for all proteins in a set of 15 arthropod genomes including 3 reference species. It can be used for comparative and deeper functional analysis of a wide range of gene functions and pathways.
Equipment or Software Used
AgBase functional annotation workflow
Funding Sources
Agricultural Research Service
0500-00093-001-00-D
Primary Article

Saha, S., Cooksey, A. M., Childers, A. K., Poelchau, M. F., & McCarthy, F. M. (2021). Workflows for rapid functional annotation of diverse arthropod genomes. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.06.12.448177

AgID: 7485855
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1522860
Product Type
Dataset
FieldValue
OSTI Identifier
ISO Topic(s)
biota
National Agricultural Library Thesaurus Term
proteome
prediction
statistics
Apis mellifera
honey bees
Drosophila melanogaster
fruit flies
Tribolium castaneum
Latrodectus hesperus
Limnephilus
Oncopeltus fasciatus
Homalodisca vitripennis
Eurytemora affinis
Agrilus planipennis
Copidosoma floridanum
parasitic wasps
Athalia rosae
Ceratitis capitata
Cimex lectularius
Varroa destructor
parasitic mites
Diaphorina citri
gene ontology
proteins
genes
Ag Data Commons Keywords
  • Genomics & Genetics
  • Genome
  • Genome annotation
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics

Suggested Citations:

(original article) Saha, S., Cooksey, A. M., Childers, A. K., Poelchau, M. F., & McCarthy, F. M. (2021). Workflows for rapid functional annotation of diverse arthropod genomes. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.06.12.448177

(dataset) Saha, Surya; Cooksey, Amanda M.; Childers, Anna K.; Poelchau, Monica F.; McCarthy, Fiona M. (2021). Functional annotation for 15 diverse arthropod genomes. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1522860. Accessed 2023-06-04.