Abstract
BackgroundCarbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.ResultsHere, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.ConclusionsCAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1571-8) contains supplementary material, which is available to authorized users.
Highlights
Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown
Genome-wide analysis of Carbohydrate Active enZymes (CAZymes) classes in plants To gain insight into the evolution of CAZyme genes across key land plant evolutionary lineages, we compared the domain content of twenty-two plant species that have been annotated in dbCAN from Phytozome by examining the number of genes containing CAZyme domains, and the frequency of CAZyme domains in these genes within each plant genome (Table 1)
The absolute frequencies of CAZy domains vary between plant genomes, we found that the proportions of the five functional CAZymes classes (GT, glycosyl hydrolase (GH), carbohydrate esterase (CE), polysaccharide lyase (PL), carbohydrate binding module (CBM)) are remarkably similar among species (Figure 1 a, b)
Summary
Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. Carbohydrate metabolism in plants is responsible for a diverse array of developmental processes, including energy metabolism, signaling, defense, cell wall (CW) structure [1], and carbohydrate-related post-translational modifications [2]. Carbohydrate biopolymers in the secondary cell walls (SCWs) of fiber cells form the bulk of woody biomass, a valuable natural resource with a variety of industrial applications, including pulp and paper, and potential biofuel production [3,4]. Cellulose and hemicelluloses are synthesized, modified, and degraded by Carbohydrate-Active enZymes (CAZymes), a group comprising of modular protein domains that are ubiquitous across all living organisms [7,8,9]. The five CAZyme classes are collected and organized into families based on amino acid sequence similarity in the CAZy database [8,13]
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