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README.md

Transcriptional roadmap to seasonal variation in wood formation of Norway spruce

Authors

Soile Jokipii-Lukkari,1,3, Nicolas Delhomme,1, Bastian Schiffthaler,2, Chanaka Mannapperuma,2, Jakob Prestele,2, Ove Nilsson,1, Nathaniel R. Street,2, Hannele Tuominen,2

Affiliations

  1. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Sveriges Lantbruksuniversitet, Umeå, Sweden
  2. Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
  3. Current address: Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland

Abstract

Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation and tracheid cell death in Norway spruce (Picea abies) woody tissues throughout one whole seasonal cycle. Simultaneously, RNA sequencing was performed in both the xylem and cambium/phloem tissues of the stem. Principal component analysis revealed gradual shifts in the transcriptomes that followed chronological order throughout the season. A notable remodulation of the transcriptome was observed in the winter, with many genes having maximal expression during the coldest months of the year. Also a highly co-expressed set of monolignol biosynthesis genes showed, in addition to a high expression during the period of secondary cell wall formation, a second peak in mid-winter. This winter peak in the expression did not trigger lignin deposition, as determined by pyrolysis–gas chromatography/mass spectrometry. Co-expression consensus network analyses suggested function of transcription factors belonging to the AS2/LOB and MYB-HB families in seasonal control of secondary cell wall formation of tracheids. Interestingly, the lifetime of the latewood tracheids stretched beyond the winter dormancy period, correlating with the lack of cell death related gene expression. The transcriptomic analyses combined with phylogenetic and microscopic analyses led also to identification of the Norway spruce genes encoding for cellulose and lignin biosynthetic genes, and putative regulators of latewood formation and tracheid cell death, providing a toolbox for further physiological and functional assays of these important phase transitions.

Content of this repository

This repository contains the custom scripts used for performing the biological quality assessment of the data, the differential expression and subsequent analyses mentioned in the manuscript.

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