PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

Abstract

With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences.

Figure 1.

The flowchart for construction of PlantTFDB 3.0.

Figure 2.

Refined family assignment rules used for TF identification and assignment. Green ellipses represent TF families and red rectangles represent DBDs. Blue rectangles denote auxiliary domains and purple rectangles denote forbidden domains. Green solid lines link families and DBDs or auxiliary domains and number ‘1’ or ‘2’ indicates number of DBDs. Red dash lines link families and forbidden domains. Families belonging to the same superfamily are arranged within rectangles or rhombi.

Figure 3.

The pipeline for construction of orthologous groups.