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A transcriptional timetable of autumn senescence

Anders Andersson1, Johanna Keskitalo2, Andreas Sjödin2, Rupali Bhalerao12, Fredrik Sterky1, Kirsten Wissel2, Karolina Tandre3, Henrik Aspeborg1, Richard Moyle3, Yasunori Ohmiya3, Rishikesh Bhalerao3, Amy Brunner4, Petter Gustafsson2, Jan Karlsson2, Joakim Lundeberg1, Ove Nilsson3, Göran Sandberg3, Steven Strauss4, Björn Sundberg3, Mathias Uhlen1, Stefan Jansson2* and Peter Nilsson1*

Author affiliations

1 Department of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden

2 Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden

3 Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden

4 Department of Forest Science, Richardson Hall, Oregon State University, Corvallis, OR 97331-5752, USA

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Citation and License

Genome Biology 2004, 5:R24  doi:

Published: 10 March 2004



We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence.


On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates.


We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.