Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon

Abstract

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.

Comparative transcriptome analysis provides key insights into gene expression pattern during the formation of nodule-like structures in Brachypodium

“…This makes it a tractable model to investigate grass roots. Also, Brachypodium is increasingly used in comparative transcriptomics studies to compare and contrast genome wide expression patterns during important biological processes (Davidson et al 2012; Huan et al 2013; Sharma et al 2017; Sibout et al 2017). One of the challenging steps in agricultural biotechnology application is to transfer findings obtained in model species such as Brachypodium and rice to crop plants without sequenced genomes.…”

“…While rice is an important model plant for tropical species, Brachypodium is an ideal model for temperate species that includes grain crops such as wheat, barley, and oats and forage grasses. Increasingly, Brachypodium is used with other grasses in comparative genomics studies to accelerate the process of gene discovery in grasses (Davidson et al 2012; Huan et al 2013; Sharma et al 2017; Sibout et al 2017). Comparative genomics facilitates identification of conserved and species-specific gene expression patterns between closely and distantly related species.…”

Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants

“…Therefore, with the increasing availability of assembled genomes, gene function prediction is currently one of the most active areas in bioinformatics. Coexpression analyses are widely used (Radivojac et al, 2013;Rhee & Mutwil, 2014;Jiang et al, 2016), and have been applied to successfully identify genes involved in plant viability (Mutwil et al, 2010), seed germination (Bassel et al, 2011), shade avoidance (Jim enez-G omez et al, 2010), cyclic electron flow (Takabayashi et al, 2009), cell division (Takahashi et al, 2008), drought sensitivity and lateral root development (Lee et al, 2010), and others (Stuart et al, 2003;Yu et al, 2003;Persson et al, 2005;Itkin et al, 2013;Proost & Mutwil, 2016;Sibout et al, 2017). Co-expression is based on the guilt-byassociation principle, which states that genes involved in the same or closely related biological processes tend to have similar expression patterns across organs, developmental stages, and biotic as well as abiotic perturbations (Usadel et al, 2009).…”

Brachypodium: A Monocot Grass Model Genus for Plant Biology

“…Through the 250 efforts of the International Brachypodium Initiative, the community aims to allow free access to genetics 251 and genomics resources among Brachypodium research groups. To this end, a B. distachyon gene 252 expression atlas was recently completed, which maps gene expression in major organs at different 253 developmental stages (Sibout et al, 2017). The gene atlas is a new, invaluable tool to study gene function 254 and to identify metabolic pathways.…”