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

Pinard D, Mizrachi E, Hefer CA, Kersting AR, Joubert F, Douglas CJ, Mansfield SD, Myburg AA - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Total gene expression levels of GT domain families across six tissue types in E. grandis. The y-axis shows the total expression investment in FPKM from raw mRNA-Seq data summed across expressed glycosyl transferase (GT) genes, while the x-axis shows the GT domain family. The depth axis is the tissue type in E. grandis for which each domain family expression level in FPKM was calculated. Light green- young leaf, dark green- mature leaf, mint green- shoot tips, red- flowers, brown-immature xylem and yellow- phloem. The expression level in FPKM for each gene can be found in Additional file 8.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4440533&req=5

Fig3: Total gene expression levels of GT domain families across six tissue types in E. grandis. The y-axis shows the total expression investment in FPKM from raw mRNA-Seq data summed across expressed glycosyl transferase (GT) genes, while the x-axis shows the GT domain family. The depth axis is the tissue type in E. grandis for which each domain family expression level in FPKM was calculated. Light green- young leaf, dark green- mature leaf, mint green- shoot tips, red- flowers, brown-immature xylem and yellow- phloem. The expression level in FPKM for each gene can be found in Additional file 8.

Mentions: The majority of GT domain families showed fairly low levels of ubiquitous expression across six tissues in E. grandis tissues (Figure 3, Additional file 9). We identified domain families that had expression levels higher in a single tissue compared to the remaining five. Of the forty-seven GT domain families present in the E. grandis genome, nine GT families (GT1, GT2, GT4, GT8, GT14, GT31, GT41, GT43, and GT47)(Figure 3) accounted for 80% of GT expression in immature xylem (Additional file 9). GT41 had the highest expression investment across all tissues (Figure 3). GT41 proteins often contain repeats of the GT41 domain, and in E. grandis the gene (Eucgr.L00641) contains seven GT41 repeats and had the highest expression of all GT41 containing proteins at >6 million FPKM in the xylem (Additional file 8). The GT41 domain occurs 241 times in the E. grandis genome, of which 120 genes containing this domain are expressed in at least one tissue. In comparison, GT1 occurs 511 times in the genome, of which 332 were expressed in at least one tissue and had lower expression investment in the immature xylem compared to the other five tissues analyzed. Thus, GT1 domains are more prevalent in the genome, and more genes containing this domain were expressed, but the magnitude of expression of these genes was considerably lower than the less abundant GT41 domain containing genes.Figure 3


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

Pinard D, Mizrachi E, Hefer CA, Kersting AR, Joubert F, Douglas CJ, Mansfield SD, Myburg AA - BMC Genomics (2015)

Total gene expression levels of GT domain families across six tissue types in E. grandis. The y-axis shows the total expression investment in FPKM from raw mRNA-Seq data summed across expressed glycosyl transferase (GT) genes, while the x-axis shows the GT domain family. The depth axis is the tissue type in E. grandis for which each domain family expression level in FPKM was calculated. Light green- young leaf, dark green- mature leaf, mint green- shoot tips, red- flowers, brown-immature xylem and yellow- phloem. The expression level in FPKM for each gene can be found in Additional file 8.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4440533&req=5

Fig3: Total gene expression levels of GT domain families across six tissue types in E. grandis. The y-axis shows the total expression investment in FPKM from raw mRNA-Seq data summed across expressed glycosyl transferase (GT) genes, while the x-axis shows the GT domain family. The depth axis is the tissue type in E. grandis for which each domain family expression level in FPKM was calculated. Light green- young leaf, dark green- mature leaf, mint green- shoot tips, red- flowers, brown-immature xylem and yellow- phloem. The expression level in FPKM for each gene can be found in Additional file 8.
Mentions: The majority of GT domain families showed fairly low levels of ubiquitous expression across six tissues in E. grandis tissues (Figure 3, Additional file 9). We identified domain families that had expression levels higher in a single tissue compared to the remaining five. Of the forty-seven GT domain families present in the E. grandis genome, nine GT families (GT1, GT2, GT4, GT8, GT14, GT31, GT41, GT43, and GT47)(Figure 3) accounted for 80% of GT expression in immature xylem (Additional file 9). GT41 had the highest expression investment across all tissues (Figure 3). GT41 proteins often contain repeats of the GT41 domain, and in E. grandis the gene (Eucgr.L00641) contains seven GT41 repeats and had the highest expression of all GT41 containing proteins at >6 million FPKM in the xylem (Additional file 8). The GT41 domain occurs 241 times in the E. grandis genome, of which 120 genes containing this domain are expressed in at least one tissue. In comparison, GT1 occurs 511 times in the genome, of which 332 were expressed in at least one tissue and had lower expression investment in the immature xylem compared to the other five tissues analyzed. Thus, GT1 domains are more prevalent in the genome, and more genes containing this domain were expressed, but the magnitude of expression of these genes was considerably lower than the less abundant GT41 domain containing genes.Figure 3

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.