RicetissueTFDB: A Genome‐Wide Identification of Tissue‐Specific Transcription Factors in Rice

Abstract

Core Ideas Validated TFs expressed in rice tissue types to study gene expression profiles in rice tissues. Tissue‐specific TFs were analyzed in different rice tissues. RicetissueTFDB integrates tissue expression characters, genomic location, and GO terms for TFs. Transcription factors (TFs) regulate plant gene expression in different tissues. To investigate TF genes in rice (Oryza sativa L.), a genome‐wide TF identification was conducted with the japonica rice genome. This study identified 3078 putative TFs in 59 families. The TF number of the top 10 TF families accounted for 58% of the 3078 rice TFs. The three largest TF families were the myeloblastosis (MYB) superfamily, basic helix–loop–helix (bHLH), and far‐red‐impaired response (FAR1), which contained 413, 228, and 210 TF members, respectively. The expression profiles of the 3078 TF genes were surveyed with the RNA sequencing (RNA‐seq) data of 13 rice tissue types. Based on these expression profiles, we validated 1087 TFs expressed in 13 rice tissue types, which accounted for 35.32% of the 3078 putative TFs. We further analyzed the tissue‐specific TFs in rice. In total, 28, 14, 14, 10, 9, 5, 5, 4, 3, 3, 2, 11, and 1 tissue‐specific TF sequences were identified in the dry seed, pistil, spikelet, aleurone, anther, ovules, embryo 25 d after pollination (DAP), seed 5 DAP, root, leaf, seed 10 DAP, shoot, and endosperm 25 DAP, respectively. Moreover, we constructed RicetissueTFDB (http://221.237.158.212:50009/index), a comprehensive and public rice TF database that integrates tissue expression characters, genomic location, and Gene Ontology (GO) terms for each TF. The RicetissueTFDB database will facilitate the identification of target TFs and the functional studies about rice TFs.

The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice

“…According to the top three most significantly enriched motifs, we found that the motifs for the binding of bHLH and C2H2 transcription factors (TFs) were more enriched in PDS-specific IP-G4s + ; in contrast, the motifs for the binding of BBRBPC and bZIP TFs were more enriched in PEG-specific IP-G4s + ( Figure 2 E). These TFs have been reported to play crucial roles in the regulation of plant growth and development and stress responses [ 62 , 63 , 64 , 65 , 66 ].…”

Identification of Candidate Genes for Salt Tolerance at Seedling Stage in Rice Using QTL-Seq and Chromosome Segment Substitution Line-Derived Population

“…In rice, the major TF families that regulate salt tolerance are well studied. These include dehydration-responsive element (DRE) binding protein (DREB), ABA-responsive element (ABRE) binding protein/factor (AREB/ABF), and NAC (NAM, ATAF1/2, CUC2) [78]. Increasing research supports the role of NAC in plant response to environmental stress conditions, including salt stress [79,80].…”

Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107

“…MYB-related transcription factors comprise a prominent subtype of MYB superfamily in plants (Du et al, 2013). Based on the previous research, there are 64, and 223 MYB-related genes in the model plant Arabidopsis and rice, respectively (Chen et al, 2006(Chen et al, , 2019. Recently, 62 genes in Physcomitrella patens (Pu et al, 2020), 138 genes in Solanum tuberosum (Liu Y. H. et al, 2020), 73 genes in Musa acuminate, and 59 genes in Musa balbisiana (Tan et al, 2020) were identified as MYB-related genes.…”