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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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Distribution of CAD genes on Populus chromosomes. The names of the chromosomes and their sizes (Mb) are indicated below each chromosome. Segmental duplicated homeologous blocks [39] are indicated with the same color. The position of genes is indicated with an arrowhead.
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Figure 1: Distribution of CAD genes on Populus chromosomes. The names of the chromosomes and their sizes (Mb) are indicated below each chromosome. Segmental duplicated homeologous blocks [39] are indicated with the same color. The position of genes is indicated with an arrowhead.

Mentions: Analysis of the physical gene distribution in the Arabidopsis and Populus genomes showed that most CAD genes were located on duplicated blocks. In Arabidopsis only one gene (AtCAD5) is not located on duplicated chromosomal blocks. Almost all of the genes are still in conserved positions within the duplicated blocks. In Populus, we found 14 of the 15 CAD genes distributed on duplicated regions. The Populus CAD genes were distributed on seven chromosomes with chromosomes I, IX, and XVI having three or more genes each (Fig. 1). PoptrCAD9 was located on a scaffold not yet assigned to a chromosome (see Additional file 1). Homologous pairs from the nine duplicated genes (PoptrCAD6, PoptrCAD11, PoptrCAD3, PoptrCAD4, PoptrCAD15, PoptrCAD16, PoptrCAD8, PoptrCAD2, and PoptrCAD5) remain in conserved positions on homeologous duplicated blocks. Duplicates of PoptrCAD1, PoptrCAD12, PoptrCAD7, and PoptrCAD14 appear to be lost from the Populus genome by an unknown gene death mechanism. PoptrCAD8, PoptrCAD16, and PoptrCAD15 seem to be generated via tandem duplications from one of the genes. Only PoptrCAD13 and PoptrCAD10 were not located on duplicated blocks.


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)

Distribution of CAD genes on Populus chromosomes. The names of the chromosomes and their sizes (Mb) are indicated below each chromosome. Segmental duplicated homeologous blocks [39] are indicated with the same color. The position of genes is indicated with an arrowhead.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Distribution of CAD genes on Populus chromosomes. The names of the chromosomes and their sizes (Mb) are indicated below each chromosome. Segmental duplicated homeologous blocks [39] are indicated with the same color. The position of genes is indicated with an arrowhead.
Mentions: Analysis of the physical gene distribution in the Arabidopsis and Populus genomes showed that most CAD genes were located on duplicated blocks. In Arabidopsis only one gene (AtCAD5) is not located on duplicated chromosomal blocks. Almost all of the genes are still in conserved positions within the duplicated blocks. In Populus, we found 14 of the 15 CAD genes distributed on duplicated regions. The Populus CAD genes were distributed on seven chromosomes with chromosomes I, IX, and XVI having three or more genes each (Fig. 1). PoptrCAD9 was located on a scaffold not yet assigned to a chromosome (see Additional file 1). Homologous pairs from the nine duplicated genes (PoptrCAD6, PoptrCAD11, PoptrCAD3, PoptrCAD4, PoptrCAD15, PoptrCAD16, PoptrCAD8, PoptrCAD2, and PoptrCAD5) remain in conserved positions on homeologous duplicated blocks. Duplicates of PoptrCAD1, PoptrCAD12, PoptrCAD7, and PoptrCAD14 appear to be lost from the Populus genome by an unknown gene death mechanism. PoptrCAD8, PoptrCAD16, and PoptrCAD15 seem to be generated via tandem duplications from one of the genes. Only PoptrCAD13 and PoptrCAD10 were not located on duplicated blocks.

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