Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis
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Date
Authors
Pinard, Desre
Mizrachi, Eshchar
Hefer, Charles Amadeus
Kersting, Anna R.
Joubert, Fourie
Douglas, Carl J.
Mansfield, Shawn D.
Myburg, Alexander Andrew
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
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.
Description
Additional file 1: Table S1. Relative standard deviation (RSD) (absolute
co-efficient of variation) between plant species.
Additional file 2: Excel file: CAZyme domain family frequency across twenty-two plant species.
Additional file 3: Figure S1. Domain family frequency distribution across twenty-two species.
Additional file 4: Figure S2. Number of CAZy domains in complex CAZy domain containing proteins across ten representative plant species.
Additional file 5: Excel file: CAZyme domain containing protein complexity summary in 10 plant species.
Additional file 6: Figure S3. Venn diagram of CAZyme domain unique combinations within complex proteins in five eudicots.
Additional file 7: Excel file: Frequency of unique CAZyme domain combinations in complex proteins in 10 plant species (in separate tabs).
Additional file 8: Excel file: Expressed CAZyme domain containing proteins (FPKM) and domain content in E. grandis.
Additional file 9: Excel file: CAZyme domain family expression in FPKM with standard deviation in E. grandis.
Additional file 10: Figure S4. GH domain family expression levels across six tissues in E. grandis in FPKM.
Additional file 11: Figure S5. PL domain family expression levels across six tissues in E. grandis in FPKM.
Additional file 12: Figure S6. CE domain family expression level across six tissues in E. grandis in FPKM.
Additional file 13: Figure S7. CBM domain family expression level across six tissues in E. grandis in FPKM.
Additional file 14: Figure S8. Comparative expression patterns of GH domain families in E. grandis and P. trichocarpa.
Additional file 15: Figure S9. Comparative expression patterns of PL domain families in E. grandis and P. trichocarpa.
Additional file 16: Figure S10. Comparative expression patterns of CE domain families in E. grandis and P. trichocarpa.
Additional file 17: Figure S11. Comparative expression patterns of CBM domain families in E. grandis and P. trichocarpa.
Additional file 18: Python script domain_counter.py: Used to count the frequency of multiple domains in all species for all families across columns. Comments included in file.
Additional file 19: Python script domain_pull.py: Used to sort gene frequency based on domain family. Comments included in file.
Additional file 2: Excel file: CAZyme domain family frequency across twenty-two plant species.
Additional file 3: Figure S1. Domain family frequency distribution across twenty-two species.
Additional file 4: Figure S2. Number of CAZy domains in complex CAZy domain containing proteins across ten representative plant species.
Additional file 5: Excel file: CAZyme domain containing protein complexity summary in 10 plant species.
Additional file 6: Figure S3. Venn diagram of CAZyme domain unique combinations within complex proteins in five eudicots.
Additional file 7: Excel file: Frequency of unique CAZyme domain combinations in complex proteins in 10 plant species (in separate tabs).
Additional file 8: Excel file: Expressed CAZyme domain containing proteins (FPKM) and domain content in E. grandis.
Additional file 9: Excel file: CAZyme domain family expression in FPKM with standard deviation in E. grandis.
Additional file 10: Figure S4. GH domain family expression levels across six tissues in E. grandis in FPKM.
Additional file 11: Figure S5. PL domain family expression levels across six tissues in E. grandis in FPKM.
Additional file 12: Figure S6. CE domain family expression level across six tissues in E. grandis in FPKM.
Additional file 13: Figure S7. CBM domain family expression level across six tissues in E. grandis in FPKM.
Additional file 14: Figure S8. Comparative expression patterns of GH domain families in E. grandis and P. trichocarpa.
Additional file 15: Figure S9. Comparative expression patterns of PL domain families in E. grandis and P. trichocarpa.
Additional file 16: Figure S10. Comparative expression patterns of CE domain families in E. grandis and P. trichocarpa.
Additional file 17: Figure S11. Comparative expression patterns of CBM domain families in E. grandis and P. trichocarpa.
Additional file 18: Python script domain_counter.py: Used to count the frequency of multiple domains in all species for all families across columns. Comments included in file.
Additional file 19: Python script domain_pull.py: Used to sort gene frequency based on domain family. Comments included in file.
Keywords
Carbohydrate active enzymes, Comparative genomics, Transcriptomics, Eucalyptus grandis, Protein domains, Wood formation, Populus trichocarpa
Sustainable Development Goals
Citation
Pinard, D, Mizrachi, E, Hefer, CA, Kersting, AR, Joubert, F, Douglas, CJ, Mansfield, SD & Myburg, AA 2015, 'Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis', BMC Genomics, vol. 16, art. no. 402, pp. 1-13.