Comparative interrrogation of the developing xylem transcriptomes of two wood-forming tissues: Populus trichocarpa and Ecualyptus grandis

Wood formation is a complex developmental process governed by genetic and environmental stimuli. Populus and Eucalyptus are fast growing, high yielding tree genera that represent ecologically and economically important species suitable for generating large amounts of lignocellulosic biomass. Comparative analysis of the developing xylem and leaf transcriptomes of Populus trichocarpa and Eucalyptus grandis trees together with phylogenetic analyses identified clusters of homologous genes preferentially expressed during xylem formation in both species. A conserved set of 336 single gene pairs show highly similar xylem preferential expression patterns, as well as evidence of high functional constraint[CH2] . Individual members of multi-gene orthologous clusters known to be involved in secondary cell wall biosynthesis also show conserved xylem expression profiles. However, species-specific expression as well as opposite (xylem vs. leaf) expression patterns observed for a subset of genes suggest subtle differences in the transcriptional regulation important for xylem development in each species. Using sequence similarity and gene expression status, we identified functional homologs likely involved in xylem developmental and biosynthetic processes in Populus and Eucalyptus. Our study suggests that while genes involved in secondary cell wall biosynthesis show high levels of gene expression conservation, differential regulation of some xylem development genes may give rise to unique xylem properties.