AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

Abstract

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated highspatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.

Different Routes for Conifer- and Sinapaldehyde and Higher Saccharification upon Deficiency in the Dehydrogenase CAD1

“…S1B). According to Sundell et al (2017), other genes sharing sequence similarity with CAD1 and CAD2 also are expressed in poplar xylem, albeit not as high as CAD1 and CAD2. Therefore, we cannot exclude the possibility that PtaCAD2 or any other CAD-like protein is responsible for the residual 15% CAD activity and that down-regulation of PtaCAD2 would result in a stronger accumulation of coniferaldehyde.…”

“…PtrCAD1 has been reported to be the only CAD gene that is highly expressed in xylem (Shi et al, 2010), although both CAD genes are highly expressed in xylem according to www.popgenie.org and Sundell et al (2017). PtrCAD1 has a higher catalytic efficiency toward the hydroxycinnamaldehydes than PtrCAD2 and, hence, is thought to play the most prominent role in lignin biosynthesis in this tissue (Shi et al, 2010;Wang et al, 2014).…”

Peptide encoding Populus CLV3/ESR‐RELATED 47 (PttCLE47) promotes cambial development and secondary xylem formation in hybrid aspen

“…For in silico gene expression analyses, expression data of PtCLE47, PtCLE24 (Potri.008G191500.1) and PtCLE28 (Potri.010G039800.1) were extracted from the ASPWOOD database (http://aspwood.popgenie.org; Sundell et al, 2017). For transcriptional analyses of PttCLE47 in different tissues of hybrid aspen, a cDNA sample set from 6-month-old trees described previously by Kucukoglu et al (2017) was used.…”

“…Poplars are deciduous, hardwood trees and widely cultivated world-wide as bioenergy feed stocks and for production of pulp, paper, packing, and woody material. Accompanied by the available sequenced genome (Tuskan et al, 2006), transformation and in vitro propagation techniques (Nilsson et al, 1992), as well as transcriptomic resources (Schrader et al, 2004;Sundell et al, 2017), it is one of the best model plants in understanding the molecular basis of tree growth and development, particularly the formation of wood. Other than the studies already mentioned, functional information regarding the roles of different CLE peptides in this important tree species is scarce.…”

Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen

“…We further explored all of the genes represented within the top 1000 rank-ordered SNPs by examining their expression profiles and, in the case of transcription factors, coexpression network neighbours during wood development (Sundell et al, 2016). Of the 293 genes assessed, 40 were not expressed during wood development.…”