DRTF: a database of rice transcription factors

Gao, Ge; Zhong, Ying-Fu; Guo, An‐Yuan; Zhu, Qihui; Tang, Wen; Zheng, Wei-Mou; Gu, Xiaocheng; Wei, Liping; Luo, Jianxun

doi:10.1093/bioinformatics/btl107

Cited by 141 publications

(108 citation statements)

References 13 publications

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“…The actual number of genes in our data set is between 2,513 (the minimum number of genes) and 2,882 (the total number of sequences). This value is greater than the predicted number of TFs present in Arabidopsis (1,922) and rice (O. sativa indica, 2,025, O. sativa japonica, 2,384; Guo et al, 2005Guo et al, , 2006 and equivalent to that reported in poplar (2,576; Zhu et al, 2007). N. tabacum is considered to be an ancient allotetraploid (2n 5 4x 5 48) resulting from an interspecific hybridization event between Nicotiana sylvestris and Nicotiana tomentosiformis (Goodspeed, 1954;Murad et al, 2002).…”

Section: Tfs In the Tobacco Genomementioning

confidence: 65%

“…Seven of the nine largest TF gene families in tobacco are very similar in size and complexity to their counterparts in Arabidopsis, rice, and poplar (Guo et al, 2005;Gao et al, 2006;Zhu et al, 2007). This allowed us to identify possible functional homologs in tobacco of genes characterized in other plant species.…”

Section: Discussionmentioning

confidence: 99%

“…Together with the organ identity gene AGAMOUS, SAP is required for the maintenance of floral identity, acting in a manner similar to AP1. Both Arabidopsis and poplar have just a single SAP gene, and it is the only family among the 64 TF families that appears to be absent in rice (Gao et al, 2006). Tobacco has at least four SAP genes (Fig.…”

Section: The Sap Familymentioning

confidence: 99%

“…All 64 of these families are also present in poplar (Populus spp. ; Zhu et al, 2007), while the monocot rice (Oryza sativa) contains only 63 families (Gao et al, 2006), missing the STERILE APETALA (SAP) family that is represented by only a single gene in both of the dicot species. Recent large-scale analyses of plant TFs have produced databases for TF studies across the entire plant kingdom (Richardt et al, 2007;Udvardi et al, 2007).…”

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confidence: 99%

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Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

Rushton

Bokowiec²,

Han³

et al. 2008

Plant Physiology

236

186

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Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco-and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.

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Section: Tfs In the Tobacco Genomementioning

confidence: 65%

Section: Discussionmentioning

confidence: 99%

Section: The Sap Familymentioning

confidence: 99%

mentioning

confidence: 99%

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Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

Rushton

Bokowiec²,

Han³

et al. 2008

Plant Physiology

236

186

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“…Of the 2384 known or annotated TF genes in the rice gnome [27], 196 (8.2%) were observed to be differentially regulated by cold in this study (Additional file 14). These TF genes include 26 AP2/EREBP, 21 bHLH, 7 HSF, 19 MYB, 12 NAC, and 17 WRKY genes.…”

Section: Resultsmentioning

confidence: 97%

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

Zhang¹,

Huang²,

Wang³

et al. 2012

BMC Genomics

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BackgroundRice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.ResultsA total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.ConclusionsGenome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

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