title: Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis.
abstract: BACKGROUND
  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. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.
  
  
  RESULTS
  Here, 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.
  
  
  CONCLUSIONS
  CAZyme 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.
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. desre.pinard@fabi.up.ac.za.
authors.forename: Desre
authors.initials: D
authors.lastname: Pinard
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. eshchar.mizrachi@fabi.up.ac.za.
authors.forename: Eshchar
authors.initials: E
authors.lastname: Mizrachi
authors.affiliation: Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. charleshefer@gmail.com.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Hefer
authors.affiliation: Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster, D48149, Germany. a.kersting@uni-muenster.de.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Kersting
authors.affiliation: Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. fourie.joubert@up.ac.za.
authors.forename: Fourie
authors.initials: F
authors.lastname: Joubert
authors.affiliation: Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada. carl.douglas@botany.ubc.ca.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.affiliation: Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. shawn.mansfield@ubc.ca.
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. zander.myburg@up.ac.za.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D050260:Carbohydrate Metabolism; D017124:Conserved Sequence; D019669:Embryophyta / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D005052:Eucalyptus / Q000201:enzymology / Q000235:genetics; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D032107:Populus / Q000201:enzymology / Q000235:genetics; D014934:Wood / Q000378:metabolism*
chemical_list: D010940:Plant Proteins