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Characterization of genes with tissue-specific differential expression patterns in Populus

Abstract

Like many plants, Populus has an evolutionary history in which several, both recent and more ancient, genome duplication events have occurred and, therefore, constitutes an excellent model system for studying the functional evolution of genes. In the present study, we have focused on the properties of genes with tissue-specific differential expression patterns in poplar. We identified the genes by analyzing digital expression profiles derived by mapping 90,000+ expressed sequence tags (ESTs) from 18 sources to the predicted genes of Populus. Our sequence analysis suggests that tissue-specific differentially expressed genes have less diverged paralogs than average, indicating that gene duplication events is an important event in the pathway leading to this type of expression pattern. The functional analysis showed that genes coding for proteins involved in processes of functional importance for the specific tissue(s) in which they are expressed and genes coding for regulatory or responsive proteins are most common among the differentially expressed genes, demonstrating that the expression differentiation process is under strong selective pressure. Thus, our data supports a model where gene duplication followed by gene specialization or expansion of the regulatory and responsive networks leads to tissue-specific differential expression patterns. We have also searched for clustering of genes with similar expression pattern into gene-expression neighborhoods within the Populus genome. However, we could not detect any major clustering among the analyzed genes with highly specific expression patterns.

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Acknowledgment

This work was supported by the Knut and Alice Wallenberg Foundation and the Swedish Foundation for Strategic Research.

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Correspondence to Bo Segerman.

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Communicated by: S. Strauss

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Table 1

List of genes identified as having a specific differential expression pattern. The columns are named as follows: “ModelID”, the name of the gene. “Upregulated in Lib”, the one-letter code for the EST library it was overrepresented (in cambial zone [AB]; active cambium [UB]; dormant cambium [UA]; tension wood [G]; wood cell death [X]; young leaves [C]; senescing leaves [I]; cold-stressed leaves [L]; dormant buds [Q]; petioles [P]; flower buds [F]; female catkins [M]; male catkins [V]). Ratio, the ratio between the observed number of ESTs and the expected. “p-value,” The p value of the Fisher test. “significance category,” the significance category based on Bonferroni correction for multiple tests were labeled with ‘*’ (5%), ‘**’ (1%), and ‘***’ (0.1%). “Total clones,” number of EST clones associated with this gene. “Lib clones,” number of EST clones associated with the library in column 2. “Closest AT,” closest Arabidopsis gene. “score,” BLASTP score toward closest Arabidopsis gene. “p val,” BLASTP p value toward closest Arabidopsis gene. “annotation,” Annotation of closest Arabidopsis gene. “GO,” gene ontology of closest Arabidopsis gene. “Broad category,” functional category assigned to this gene. “2nd category,” second level of functional category (PDF 440 kb).

Fig. 1

Complement to Fig. 5. Functions of the up-regulated genes. The functions of the identified genes were divided into broad categories, and their distribution in each library was plotted. a Protein biosynthesis/folding, b degradation/hydrolysis, c intracellular structure/storage, d transport/maintainment, e metabolism, f development/aging, g transcription, h response(PDF 559 kb)

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Segerman, B., Jansson, S. & Karlsson, J. Characterization of genes with tissue-specific differential expression patterns in Populus . Tree Genetics & Genomes 3, 351–362 (2007). https://doi.org/10.1007/s11295-006-0077-6

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  • DOI: https://doi.org/10.1007/s11295-006-0077-6

Keywords

  • Tissue-specific differential expression pattern
  • Gene duplication
  • Expression neighborhood