DPTF: a database of poplar transcription factors

Zhu, Qihui; Guo, An‐Yuan; Gao, Ge; Zhong, Ying-Fu; Xu, Meng; Huang, Minren; Luo, Jianxun

doi:10.1093/bioinformatics/btm113

Cited by 90 publications

(57 citation statements)

References 12 publications

(10 reference statements)

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“…In an attempt to demonstrate the reliability of the identified genes, keyword search with NAM against NCBI nucleotide database was performed, resulting in 153 members which were all included in the NACs identified above. In comparison to the NAC gene family in PlnTFDB http://plntfdb.bio.uni-potsdam.de/v3.0/[3] and DPTF http://dptf.cbi.pku.edu.cn/[58], in which 167 and 172 members were proposed respectively, the 170 gene loci revealed in the present study were roughly in agreement with the former. Then, the discrepancy loci identified in our studies with the two databases mentioned above were further scrutinized to see if any misannotations were inferred.…”

Section: Resultssupporting

confidence: 81%

“…Hidden Markov Model (HMM) profile of NAC domain (PF02365) downloaded from Protein family (Pfam) http://pfam.sanger.ac.uk/ was exploited for the identification of the NAC genes from Populus genome using HMMER (v 2.3.2) [89]. All non-redundant hits with expected values less than 1.0 were collected and then compared with the NAC family in PlnTFDB http://plntfdb.bio.uni-potsdam.de/v3.0/[3] and DPTF http://dptf.cbi.pku.edu.cn/[58]. As for the incorrectly predicted genes, manual reannotation was performed using online web server FGENESH http://linux1.softberry.com/berry.phtml[59].…”

Section: Methodsmentioning

confidence: 99%

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Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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Section: Resultssupporting

confidence: 81%

Section: Methodsmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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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: 58%

“…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%

“…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

241

179

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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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Populus Resources and Bioinformatics

Street

Tsai

2009

Genetics and Genomics of Populus

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DPTF: a database of poplar transcription factors

Cited by 90 publications

References 12 publications

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

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

Populus Resources and Bioinformatics

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