Abstract

Summary Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes.Microarray analyses were used to: identify and functionally characterize groups of co‐expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation.We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue‐based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC‐7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup‐shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation.Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure.

Highlights

  • Transcriptome analysis is among the most widely used largescale experimental approaches to investigate genome function and to help annotate genome sequences (Pickrell et al, 2010; Prasad et al, 2013; Ellison et al, 2014)

  • We found that 95% of the conserved xylem and phelloderm preferential genes were distributed among all coexpression groups, indicating that their modular organization is represented by diverse expression profiles (Fig. 4)

  • Our findings describe the modular organization of the white spruce transcriptome, which we divided into invariant genes and coexpression groups of variable genes across tissues

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Summary

Introduction

Transcriptome analysis is among the most widely used largescale experimental approaches to investigate genome function and to help annotate genome sequences (Pickrell et al, 2010; Prasad et al, 2013; Ellison et al, 2014). CDNA and transcriptome sequencing in conifers has been ongoing for over 15 yr (Allona et al, 1998), has led to many functional investigations, and produced outcomes that enable genetic mapping research, association studies and investigations of evolutionary adaptation (MacKay et al, 2012). Despite this extensive body of work, a general framework describing transcriptome organization in conifers is lacking and would help to develop a more unified understanding of genome function

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