The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

Abstract

The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an extensive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.

Figure 1.

Overview of TAIR genome releases. (A) Bar graph displaying the number of annotation updates made in each of the 5 TAIR releases. Colored bars represent four different classes of updates: updated genes (light green), genes with CDS updates (orange), new genes (yellow) and new splice variants (dark green). (B) Table comparing the TAIR genome releases by types of data and prediction tools used, areas of focus and genome sequence updates. The red line separating TAIR8 from TAIR9 indicates that coordinates of most genes shifted in the TAIR9 release, as a consequence of the integration of 341 Indels, and the normalization of previously identified sequence contaminations to a standard length of 100 bp. A liftover tool is available at ftp://ftp.arabidopsis.org/home/tair/Software/UpdateCoord/ for updating coordinates of objects mapped to TAIR8 or earlier releases.