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Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa.

Duan W, Song X, Liu T, Huang Z, Ren J, Hou X, Du J, Li Y - Genome Biol Evol (2014)

Bottom Line: Ascorbic acid (AsA) is an important antioxidant in plants and an essential vitamin for humans.The nucleobase-ascorbate transporter (NAT) gene family and AsA l-galactose pathway genes were also compared among plant species.In summary, this study provides genome-wide insights into evolutionary history and mechanisms of AsA-related genes following whole-genome triplication in B. rapa.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, People's Republic of China.

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Expression patterns analysis of all AsA-related genes in Arabidopsis thaliana and Brassica rapa. Expression levels were analyzed in root, stem, leaf, and flower tissues. (A) The A. thaliana expression profiling was analyzed using the AtGenExpress Visualization Tool with mean-normalized values (supplementary table S10, Supplementary Material online). (B) Heat map of RNA-Seq data for Brassica rapa AsA-related genes. Gene expression FPKM values were analyzed. The bar at the bottom of each heat map represents relative expression values (supplementary table S11, Supplementary Material online). (C) Venn diagram showing the numbers of AsA-related genes with similar and different expression patterns in A. thaliana and B. rapa; those gene names are colored red in (A) and (B).
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evu293-F8: Expression patterns analysis of all AsA-related genes in Arabidopsis thaliana and Brassica rapa. Expression levels were analyzed in root, stem, leaf, and flower tissues. (A) The A. thaliana expression profiling was analyzed using the AtGenExpress Visualization Tool with mean-normalized values (supplementary table S10, Supplementary Material online). (B) Heat map of RNA-Seq data for Brassica rapa AsA-related genes. Gene expression FPKM values were analyzed. The bar at the bottom of each heat map represents relative expression values (supplementary table S11, Supplementary Material online). (C) Venn diagram showing the numbers of AsA-related genes with similar and different expression patterns in A. thaliana and B. rapa; those gene names are colored red in (A) and (B).

Mentions: AsA metabolism-related enzymes, such as ascorbate oxidase (AO), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDAR), are normally encoded by genes from multigene families (Chen et al. 2003). Their cycle can be depicted as a triangular loop (fig. 7). In this study, their phylogenetic relationships and expression patterns were analyzed (fig. 7). The proteins that shared a clade were closely related, indicating that they were functionally similar, but some of their expression patterns were different. Two homologous members for DHAR, MDAR, APX, and AO genes, respectively, in B. rapa were found with little expression (fig. 7). It indicated that their function may be lost during the Brassica-specific WGT event. The tissue-specific expression patterns of these genes were found in A. thaliana, whereas high expression in all tissues was found in 11 B. rapa genes (fig. 8). The different expression patterns in this multigene family may help plants adapt to different environments.Fig. 7.—


Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa.

Duan W, Song X, Liu T, Huang Z, Ren J, Hou X, Du J, Li Y - Genome Biol Evol (2014)

Expression patterns analysis of all AsA-related genes in Arabidopsis thaliana and Brassica rapa. Expression levels were analyzed in root, stem, leaf, and flower tissues. (A) The A. thaliana expression profiling was analyzed using the AtGenExpress Visualization Tool with mean-normalized values (supplementary table S10, Supplementary Material online). (B) Heat map of RNA-Seq data for Brassica rapa AsA-related genes. Gene expression FPKM values were analyzed. The bar at the bottom of each heat map represents relative expression values (supplementary table S11, Supplementary Material online). (C) Venn diagram showing the numbers of AsA-related genes with similar and different expression patterns in A. thaliana and B. rapa; those gene names are colored red in (A) and (B).
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4316640&req=5

evu293-F8: Expression patterns analysis of all AsA-related genes in Arabidopsis thaliana and Brassica rapa. Expression levels were analyzed in root, stem, leaf, and flower tissues. (A) The A. thaliana expression profiling was analyzed using the AtGenExpress Visualization Tool with mean-normalized values (supplementary table S10, Supplementary Material online). (B) Heat map of RNA-Seq data for Brassica rapa AsA-related genes. Gene expression FPKM values were analyzed. The bar at the bottom of each heat map represents relative expression values (supplementary table S11, Supplementary Material online). (C) Venn diagram showing the numbers of AsA-related genes with similar and different expression patterns in A. thaliana and B. rapa; those gene names are colored red in (A) and (B).
Mentions: AsA metabolism-related enzymes, such as ascorbate oxidase (AO), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDAR), are normally encoded by genes from multigene families (Chen et al. 2003). Their cycle can be depicted as a triangular loop (fig. 7). In this study, their phylogenetic relationships and expression patterns were analyzed (fig. 7). The proteins that shared a clade were closely related, indicating that they were functionally similar, but some of their expression patterns were different. Two homologous members for DHAR, MDAR, APX, and AO genes, respectively, in B. rapa were found with little expression (fig. 7). It indicated that their function may be lost during the Brassica-specific WGT event. The tissue-specific expression patterns of these genes were found in A. thaliana, whereas high expression in all tissues was found in 11 B. rapa genes (fig. 8). The different expression patterns in this multigene family may help plants adapt to different environments.Fig. 7.—

Bottom Line: Ascorbic acid (AsA) is an important antioxidant in plants and an essential vitamin for humans.The nucleobase-ascorbate transporter (NAT) gene family and AsA l-galactose pathway genes were also compared among plant species.In summary, this study provides genome-wide insights into evolutionary history and mechanisms of AsA-related genes following whole-genome triplication in B. rapa.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, People's Republic of China.

Show MeSH
Related in: MedlinePlus