Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis

BMC Genomics

Alexander A Myburg³  Shawn D Mansfield⁵  Carl J Douglas⁴  Fourie Joubert²  Anna R Kersting¹  Charles A Hefer²  Eshchar Mizrachi³  Desre Pinard³ 

[1] Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster D48149, Germany;Centre for Bioinformatics and Computational Biology, Genomics Research Institute (GRI), University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South Africa;Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South Africa;Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver V6T 1Z4, BC, Canada;Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver V6T 1Z4, BC, Canada

关键词: Populus trichocarpa;    Wood formation;    Protein domains;    Eucalyptus grandis;    Transcriptomics;    Comparative genomics;    Carbohydrate active enzymes;   

Others  :  1203905
DOI  :  10.1186/s12864-015-1571-8

 received in 2014-10-17, accepted in 2015-04-23,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Pinard et al.; licensee BioMed Central.

【 图 表 】

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