UPSC‐BASE –<i>Populus</i> transcriptomics online

Sjödin, Andreas; Bylesjö, Max; Skogström, Oskar; Eriksson, Daniel; Nilsson, Peter; Rydén, Patrik; Jansson, Stefan; Karlsson, Jan

doi:10.1111/j.1365-313x.2006.02920.x

Cited by 52 publications

(66 citation statements)

References 72 publications

(115 reference statements)

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“…To gain more insight into the expression patterns of NAC genes, a comprehensive expression analysis was further performed by utilizing the publicly available microarray data for Populus . Firstly, we re-analyzed the collections of microarray data from wood-formation series available at PopGenIE, a database repository of transcriptomics data available for Populus [82,83]. Distinct expression profiles were identified for a total of 29 NAC genes (Figure 6 and Additional file 9), whereas no corresponding probe sets were available for the remaining NACs in the datasets.…”

Section: Resultsmentioning

confidence: 99%

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: Resultsmentioning

confidence: 99%

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

et al. 2010

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“…Data have been deposited in the UPSC-BASE Populus transcriptomics online (http://www.upscbase.db.umu.se/) (Sjö din et al, 2006) under experiment number 0015.…”

Section: Microarray Data Depositionmentioning

confidence: 99%

Downregulation of Cinnamoyl-Coenzyme A Reductase in Poplar: Multiple-Level Phenotyping Reveals Effects on Cell Wall Polymer Metabolism and Structure

et al. 2007

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Cinnamoyl-CoA reductase (CCR) catalyzes the penultimate step in monolignol biosynthesis. We show that downregulation of CCR in transgenic poplar (Populus tremula 3 Populus alba) was associated with up to 50% reduced lignin content and an orange-brown, often patchy, coloration of the outer xylem. Thioacidolysis, nuclear magnetic resonance (NMR), immunocytochemistry of lignin epitopes, and oligolignol profiling indicated that lignin was relatively more reduced in syringyl than in guaiacyl units. The cohesion of the walls was affected, particularly at sites that are generally richer in syringyl units in wild-type poplar. Ferulic acid was incorporated into the lignin via ether bonds, as evidenced independently by thioacidolysis and by NMR. A synthetic lignin incorporating ferulic acid had a red-brown coloration, suggesting that the xylem coloration was due to the presence of ferulic acid during lignification. Elevated ferulic acid levels were also observed in the form of esters. Transcript and metabolite profiling were used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. Both methods suggested reduced biosynthesis and increased breakdown or remodeling of noncellulosic cell wall polymers, which was further supported by Fourier transform infrared spectroscopy and wet chemistry analysis. The reduced levels of lignin and hemicellulose were associated with an increased proportion of cellulose. Furthermore, the transcript and metabolite profiling data pointed toward a stress response induced by the altered cell wall structure. Finally, chemical pulping of wood derived from 5-year-old, field-grown transgenic lines revealed improved pulping characteristics, but growth was affected in all transgenic lines tested.

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“…In order to study the gene expression of KNOX genes in poplar we identified nine ESTs (expressed sequence tags) within 17 345 poplar gene models in the UPSC 297 BASE (Sjödin et al, 2006). The nine ESTs correspond to six different gene models ( Figure 2D).…”

Section: Resultsmentioning

confidence: 99%

“…The Pearson Correlation was applied to estimate the distance between nodes. Expression data for the poplar KNOX genes was obtained form the UPSC BASE (Sjödin et al, 2006) or directly from the respective publications.…”

Section: Introductionmentioning

confidence: 99%

Review of forests, wood products and wood biotechnology of Iran and Germany - Part III

2009

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UPSC‐BASE –Populus transcriptomics online

Cited by 52 publications

References 72 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

Downregulation of Cinnamoyl-Coenzyme A Reductase in Poplar: Multiple-Level Phenotyping Reveals Effects on Cell Wall Polymer Metabolism and Structure

Review of forests, wood products and wood biotechnology of Iran and Germany - Part III

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