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The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression.

Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto DS, Yellanki P, Carlson JE - BMC Plant Biol. (2009)

Bottom Line: CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II.The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae.Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA. aub14@psu.edu

ABSTRACT

Background: Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus.

Results: The phylogenetic analyses showed that CAD genes fall into three main classes (clades), one of which is represented by CAD sequences from gymnosperms and angiosperms. The other two clades are represented by sequences only from angiosperms. All Populus CAD genes, except PoptrCAD 4 are distributed in Class II and Class III. CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II. Most of the CAD genes are physically distributed on duplicated blocks and are still in conserved locations on the homeologous duplicated blocks. Promoter analysis of CAD genes revealed several motifs involved in gene expression modulation under various biological and physiological processes. The CAD genes showed different expression patterns in poplar with only two genes preferentially expressed in xylem tissues during lignin biosynthesis.

Conclusion: The phylogeny of CAD genes suggests that the radiation of this gene family may have occurred in the early ancestry of angiosperms. Gene distribution on the chromosomes of Populus showed that both large scale and tandem duplications contributed significantly to the CAD gene family expansion. The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae. Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II. The other CAD genes from Class II and Class III may function in plant tissues under biotic stresses. The conservation of most duplicated CAD genes, the differential distribution of motifs in their promoter regions, and the divergence of their expression profiles in various tissues of Populus plants indicate that genes in the CAD family have evolved tissue-specialized expression profiles and may have divergent functions.

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Intron-exon structures of CAD genes from Populus. Exons and introns are indicated by open boxes and lines respectively. Numbers above boxes indicate the exon sizes. The intron sizes are not to scale. The names of CAD genes and intron-exon structure are indicated at the left and right sides respectively.
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Figure 2: Intron-exon structures of CAD genes from Populus. Exons and introns are indicated by open boxes and lines respectively. Numbers above boxes indicate the exon sizes. The intron sizes are not to scale. The names of CAD genes and intron-exon structure are indicated at the left and right sides respectively.

Mentions: Gene structure analysis of Populus CAD genes (Fig. 2) revealed the existence of three patterns of intron-exon structures. Pattern 1 (PoptrCAD5, PoptrCAD10, PoptrCAD3, PoptrCAD9, PoptrCAD1, PoptrCAD13, PoptrCAD8, PoptrCAD6, PoptrCAD15, and PoptrCAD16), pattern 2 (PoptrCAD4), and pattern 3 (PoptrCAD2, PoptrCAD11, PoptrCAD12, PoptrCAD14, and PoptrCAD7) were composed by 5, 5, and 6 exons, respectively. Pattern 1 and pattern 2 present a difference in length of exon 3 and exon 4. Genes within these patterns present a similar number and size of exons. All Populus duplicated genes show a similar structure. PoptrCAD16 and PoptrCAD8, which may have risen from PoptrCAD15 by tandem duplication, also showed the same structure. While the intron length is conserved between some homeologous introns, others exhibit a great deal of variation. The increase in length could be due to transposable element insertions. Homeologous duplicate pairs (PoptrCAD11 – PoptrCAD2, PoptrCAD5 – PoptrCAD3, and PoptrCAD6 – PoptrCAD8) genes also show similar structure between homologs (Fig. 2).


The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression.

Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto DS, Yellanki P, Carlson JE - BMC Plant Biol. (2009)

Intron-exon structures of CAD genes from Populus. Exons and introns are indicated by open boxes and lines respectively. Numbers above boxes indicate the exon sizes. The intron sizes are not to scale. The names of CAD genes and intron-exon structure are indicated at the left and right sides respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2662859&req=5

Figure 2: Intron-exon structures of CAD genes from Populus. Exons and introns are indicated by open boxes and lines respectively. Numbers above boxes indicate the exon sizes. The intron sizes are not to scale. The names of CAD genes and intron-exon structure are indicated at the left and right sides respectively.
Mentions: Gene structure analysis of Populus CAD genes (Fig. 2) revealed the existence of three patterns of intron-exon structures. Pattern 1 (PoptrCAD5, PoptrCAD10, PoptrCAD3, PoptrCAD9, PoptrCAD1, PoptrCAD13, PoptrCAD8, PoptrCAD6, PoptrCAD15, and PoptrCAD16), pattern 2 (PoptrCAD4), and pattern 3 (PoptrCAD2, PoptrCAD11, PoptrCAD12, PoptrCAD14, and PoptrCAD7) were composed by 5, 5, and 6 exons, respectively. Pattern 1 and pattern 2 present a difference in length of exon 3 and exon 4. Genes within these patterns present a similar number and size of exons. All Populus duplicated genes show a similar structure. PoptrCAD16 and PoptrCAD8, which may have risen from PoptrCAD15 by tandem duplication, also showed the same structure. While the intron length is conserved between some homeologous introns, others exhibit a great deal of variation. The increase in length could be due to transposable element insertions. Homeologous duplicate pairs (PoptrCAD11 – PoptrCAD2, PoptrCAD5 – PoptrCAD3, and PoptrCAD6 – PoptrCAD8) genes also show similar structure between homologs (Fig. 2).

Bottom Line: CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II.The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae.Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA. aub14@psu.edu

ABSTRACT

Background: Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus.

Results: The phylogenetic analyses showed that CAD genes fall into three main classes (clades), one of which is represented by CAD sequences from gymnosperms and angiosperms. The other two clades are represented by sequences only from angiosperms. All Populus CAD genes, except PoptrCAD 4 are distributed in Class II and Class III. CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II. Most of the CAD genes are physically distributed on duplicated blocks and are still in conserved locations on the homeologous duplicated blocks. Promoter analysis of CAD genes revealed several motifs involved in gene expression modulation under various biological and physiological processes. The CAD genes showed different expression patterns in poplar with only two genes preferentially expressed in xylem tissues during lignin biosynthesis.

Conclusion: The phylogeny of CAD genes suggests that the radiation of this gene family may have occurred in the early ancestry of angiosperms. Gene distribution on the chromosomes of Populus showed that both large scale and tandem duplications contributed significantly to the CAD gene family expansion. The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae. Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II. The other CAD genes from Class II and Class III may function in plant tissues under biotic stresses. The conservation of most duplicated CAD genes, the differential distribution of motifs in their promoter regions, and the divergence of their expression profiles in various tissues of Populus plants indicate that genes in the CAD family have evolved tissue-specialized expression profiles and may have divergent functions.

Show MeSH
Related in: MedlinePlus