Reiser, L. | bioRxiv Science

bioRxiv2023

The Arabidopsis Information Resource in 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a gold standard functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resources role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used Gene Ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function, and (2) the set of unknown genes. Currently, 74% of the proteome has been annotated to at least one Gene Ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries. Article SummaryThe Arabidopsis Information Resource (TAIR, www.arabidopsis.org) is a comprehensive website about Arabidopsis thaliana, a small plant thats very easy to grow and analyze in the laboratory and is used to understand how many other plants function. We share our progress in data collection and organization, website and tool improvement, and our involvement in community projects.

plant biology↗

bioRxiv2022

An updated nomenclature for plant ribosomal protein genes

Ban et al. (2014) proposed a nomenclature for ribosomal proteins (r-proteins) that reflects the current understanding of ribosomal protein evolution. In the past few years, this nomenclature has been widely adopted among biomedical researchers and microbiologists. This homology-based r-protein nomenclature has not been as widely adopted among plant biologists, however, presumably because r-protein nomenclature is much more complicated in plants due to gene duplication. Here, we propose compatible upgrades to the homology-guided nomenclature proposed by Ban et al. (2014) so that this naming system can be adopted for widespread use in the plant biology community. We note that Lan et al. (2022) recently proposed updated nomenclature for plant cytosolic ribosomal proteins, focused on Arabidopsis and rice. The nomenclature outlined here is an extension of that proposed by Lan et al. (2022), expanding to include organellar ribosomes and additional species, with the intent that this nomenclature can serve as a template to guide future plant genome annotations. A more detailed comparison highlighting how this naming system builds on the Ban et al. (2014) and Lan et al. (2022) nomenclatures is offered below. At this time, we request community feedback on this proposed nomenclature so that the naming system ultimately chosen represents a broad consensus. Feedback can be communicated to the this working group at plantribosome@gmail.com before July 25th, 2022. Coauthors of this letter and anyone in the scientific community expressing significant interest will then discuss this feedback as a group, reach a consensus agreement, and communicate the updated nomenclature rules through a letter to the editor (expected to be published at The Plant Cell) and the databases at TAIR and MaizeGDB.

plant biology↗