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ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species
Victor Zeng1, Cassandra G Extavour
1Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
A new database, ASGARD, provides a searchable repository for arthropod transcriptome data, addressing the challenge of genomic analysis for non-model organisms. This resource facilitates research in developmental biology, evolutionary biology, and comparative genomics.
Area of Science:
- Genomics and Bioinformatics
- Developmental Biology and Evolutionary Biology
Background:
- Next-generation sequencing (NGS) has advanced genomic research, but bottlenecks now exist in data annotation, analysis, and accessibility.
- Research communities studying organisms without sequenced genomes face significant challenges in utilizing available sequence data.
Purpose of the Study:
- To introduce the Assembled Searchable Giant Arthropod Read Database (ASGARD), a novel repository and search engine for arthropod transcriptomic data.
- To provide a centralized resource for researchers working on arthropods lacking sequenced genomes, facilitating comparative genomics and phylogenomics.
Main Methods:
- ASGARD was populated with de novo assembled transcriptomes from key arthropod species, including Oncopeltus fasciatus, Gryllus bimaculatus, and Parhyale hawaiensis.
- Transcriptomes were annotated for orthology, coding regions, protein domains, and Gene Ontology (GO) terms.
- The database was developed with user-friendly features, including auto-completion, sequence download, and links to external data.
Main Results:
- ASGARD enables searching of arthropod transcriptome assemblies by orthology, GO terms, or Basic Local Alignment Search Tool (BLAST).
- The database offers direct links to NCBI data, graphical domain visualization, and sequence download capabilities.
- Demonstrated utility with transcriptomes from milkweed bug, cricket, and amphipod crustacean.
Conclusions:
- ASGARD serves as a valuable, one-stop resource for accessing and analyzing multi-species annotated transcriptome data from emerging model arthropods.
- The database supports diverse research fields, including developmental biology, evolutionary biology, ecology, comparative genomics, and phylogenomics.
- ASGARD is expected to accelerate research by improving accessibility and analysis of genomic data for understudied arthropod species.
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