Open Access Research

A genomic approach to investigate developmental cell death in woody tissues of Populus trees

Charleen Moreau1, Nikolay Aksenov1, Maribel García Lorenzo2, Bo Segerman1, Christiane Funk2, Peter Nilsson3, Stefan Jansson1 and Hannele Tuominen1*

Author Affiliations

1 Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden

2 Department of Biochemistry, Umeå University, SE-901 87 Umeå, Sweden

3 Department of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-10691, Stockholm, Sweden

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Genome Biology 2005, 6:R34  doi:10.1186/gb-2005-6-4-r34

Published: 22 March 2005

Abstract

Background

Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers.

Results

One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences.

Conclusions

In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.