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 five CAZyme domain classes across six tissues in E. grandis. The y-axis represents the mRNA-Seq expression data in FPKM, and the x-axis the tissue type analyzed. The average expression data in FPKM for each gene can be found in Additional file 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Total gene expression levels of five CAZyme domain classes across six tissues in E. grandis. The y-axis represents the mRNA-Seq expression data in FPKM, and the x-axis the tissue type analyzed. The average expression data in FPKM for each gene can be found in Additional file 2.

Mentions: The newly sequenced genome of E. grandis [37] as well as RNA-sequencing data for several tissues and organs [48] allowed a functional genomics investigation of CAZyme containing genes. Expression profiling across six tissues in E. grandis showed that of the 2,542 CAZyme-domain containing genes in the E. grandis genome, 80.5% (2,044) are expressed in at least one tissue (Additional file 8). The relative proportions of transcript abundance for each CAZyme domain class were similar across tissues (Figure 2), although the expression of GH and GT domain classes were proportionally higher in the immature xylem. GTs constitute 44.5% of expression investment of CAZyme domain containing genes in the immature xylem vs. 35.9% in the young leaf. GHs account for 39.8% of the transcript abundance of CAZyme domain containing genes in the immature xylem, and 29.7% in the young leaf (Figure 2). CE domain family expression was proportionally lower in the phloem and immature xylem compared to the young leaf, mature leaf, flowers and shoot tips, making up 7% of the total CAZyme expression investment in the immature xylem and 20.3% in the young leaf. Variation at the level of individual CAZyme domain families was observed, and is discussed below.Figure 2


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 five CAZyme domain classes across six tissues in E. grandis. The y-axis represents the mRNA-Seq expression data in FPKM, and the x-axis the tissue type analyzed. The average expression data in FPKM for each gene can be found in Additional file 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Total gene expression levels of five CAZyme domain classes across six tissues in E. grandis. The y-axis represents the mRNA-Seq expression data in FPKM, and the x-axis the tissue type analyzed. The average expression data in FPKM for each gene can be found in Additional file 2.
Mentions: The newly sequenced genome of E. grandis [37] as well as RNA-sequencing data for several tissues and organs [48] allowed a functional genomics investigation of CAZyme containing genes. Expression profiling across six tissues in E. grandis showed that of the 2,542 CAZyme-domain containing genes in the E. grandis genome, 80.5% (2,044) are expressed in at least one tissue (Additional file 8). The relative proportions of transcript abundance for each CAZyme domain class were similar across tissues (Figure 2), although the expression of GH and GT domain classes were proportionally higher in the immature xylem. GTs constitute 44.5% of expression investment of CAZyme domain containing genes in the immature xylem vs. 35.9% in the young leaf. GHs account for 39.8% of the transcript abundance of CAZyme domain containing genes in the immature xylem, and 29.7% in the young leaf (Figure 2). CE domain family expression was proportionally lower in the phloem and immature xylem compared to the young leaf, mature leaf, flowers and shoot tips, making up 7% of the total CAZyme expression investment in the immature xylem and 20.3% in the young leaf. Variation at the level of individual CAZyme domain families was observed, and is discussed below.Figure 2

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.