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Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis).

Guo F, Yu H, Xu Q, Deng X - BMC Plant Biol. (2015)

Bottom Line: The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo.Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.

Results: High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.

Conclusions: This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

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Histogram of gene ontology classification. The results are summarized in three main categories: molecular function, biological process and cellular component. The right Y-axis indicates the number of genes in a category. The left Y-axis indicates the percentage of a specific category of genes in that main category.
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Fig3: Histogram of gene ontology classification. The results are summarized in three main categories: molecular function, biological process and cellular component. The right Y-axis indicates the number of genes in a category. The left Y-axis indicates the percentage of a specific category of genes in that main category.

Mentions: These DEGs may be involved in different functions. Gene ontology (GO) is an international standardized gene functional classification system that describes the properties of genes and their products in any organism. To understand the functions of the 303 DEGs, we mapped them to the three GO ontologies, including molecular function, cellular component, and biological process (Figure 3). According to cellular component, the most abundant DEGs were involved in “membrane” (9.2%), “cell” (5.3%) and “cell part” (5.3%). From the perspective of biological process, the DEGs were involved in “metabolic process” (28.4%), “cellular process” (20.8%), “organic substance metabolic process” (18.5%), “primary metabolic process” (17.8%) and “cellular metabolic process” (13.9%). In terms of molecular function, the genes were dominant in “catalytic activity” (31.4%), “binding” (24.4%), “ion binding” (15.5%), “heterocyclic compound binding” (13.5%) and “organic cyclic compound binding” (13.5%). In addition, the whole genome background was examined by GO category enrichment analysis (P-value ≤ 0.05). Three cellular component terms were significantly enriched in the up-regulated genes, including microtubule cytoskeleton, cytoskeletal part and cytoskeleton. To further understand the biological functions of these genes, KEGG (http://www.genome.jp/kegg/) ontology assignments were used to classify their functional annotations. All the 303 DEGs were assigned to 52 KEGG pathways. Among the pathways, carbon metabolism, starch and sucrose metabolism, biosynthesis of amino acids, and a few others were highly represented (Table 3).Figure 3


Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis).

Guo F, Yu H, Xu Q, Deng X - BMC Plant Biol. (2015)

Histogram of gene ontology classification. The results are summarized in three main categories: molecular function, biological process and cellular component. The right Y-axis indicates the number of genes in a category. The left Y-axis indicates the percentage of a specific category of genes in that main category.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4352283&req=5

Fig3: Histogram of gene ontology classification. The results are summarized in three main categories: molecular function, biological process and cellular component. The right Y-axis indicates the number of genes in a category. The left Y-axis indicates the percentage of a specific category of genes in that main category.
Mentions: These DEGs may be involved in different functions. Gene ontology (GO) is an international standardized gene functional classification system that describes the properties of genes and their products in any organism. To understand the functions of the 303 DEGs, we mapped them to the three GO ontologies, including molecular function, cellular component, and biological process (Figure 3). According to cellular component, the most abundant DEGs were involved in “membrane” (9.2%), “cell” (5.3%) and “cell part” (5.3%). From the perspective of biological process, the DEGs were involved in “metabolic process” (28.4%), “cellular process” (20.8%), “organic substance metabolic process” (18.5%), “primary metabolic process” (17.8%) and “cellular metabolic process” (13.9%). In terms of molecular function, the genes were dominant in “catalytic activity” (31.4%), “binding” (24.4%), “ion binding” (15.5%), “heterocyclic compound binding” (13.5%) and “organic cyclic compound binding” (13.5%). In addition, the whole genome background was examined by GO category enrichment analysis (P-value ≤ 0.05). Three cellular component terms were significantly enriched in the up-regulated genes, including microtubule cytoskeleton, cytoskeletal part and cytoskeleton. To further understand the biological functions of these genes, KEGG (http://www.genome.jp/kegg/) ontology assignments were used to classify their functional annotations. All the 303 DEGs were assigned to 52 KEGG pathways. Among the pathways, carbon metabolism, starch and sucrose metabolism, biosynthesis of amino acids, and a few others were highly represented (Table 3).Figure 3

Bottom Line: The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo.Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.

Results: High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.

Conclusions: This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

Show MeSH