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High-throughput, Robust and Highly Time-flexible Method for Surface Sterilization of Arabidopsis Seeds

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The Arabidopsis Information Resource in 2024.

Leonore Reiser¹, Erica Bakker¹, Sabarinath Subramaniam¹

¹Phoenix Bioinformatics, Newark, CA 94560, USA.

|March 8, 2024

Summary

The Arabidopsis Information Resource curates gene function data for Arabidopsis thaliana, with 74% of its proteome annotated. This highlights knowledge gaps for unannotated genes, guiding future research.

Keywords:

biocuration community resource model organism database plant genomics

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Area of Science:

Plant genomics
Bioinformatics
Functional genomics

Background:

The Arabidopsis Information Resource (TAIR) has curated Arabidopsis thaliana genome data since 1999.
TAIR integrates experimental gene function information from literature into controlled vocabulary annotations.
The resource aims to be a "gold standard" for functional annotation and a hub for community collaboration.

Purpose of the Study:

To provide an update on TAIR's biocuration and modernization efforts.
To assess the current state of Arabidopsis gene function knowledge using Gene Ontology (GO) annotations.
To identify and highlight "unknown" genes with no functional annotation or experimental support.

Main Methods:

Utilizing Gene Ontology (GO) annotations to evaluate known and unknown Arabidopsis gene functions.
Reviewing ongoing biocuration work and infrastructure modernization, including the implementation of JBrowse2.
Tracking community activities, such as genome structural reannotation efforts.

Main Results:

Currently, 74% of the Arabidopsis thaliana proteome is annotated with at least one GO term.
Half of the annotated loci have experimental support for molecular function, biological process, or cellular component.
A significant portion of the genome remains functionally unannotated, representing knowledge gaps.

Conclusions:

TAIR continues to be a vital resource for Arabidopsis research, providing curated functional annotations.
The assessment of GO annotations reveals the extent of current knowledge and identifies areas for future investigation.
Highlighting unannotated genes serves to direct research efforts towards novel discoveries and understanding gene function.