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Transcriptome profiling provides new insights into the formation of floral scent in Hedychium coronarium.

Yue Y, Yu R, Fan Y - BMC Genomics (2015)

Bottom Line: The de novo assembly resulted in a transcriptome with 65,591 unigenes, 50.90% of which were annotated using public databases.GO term classification and KEGG pathway analysis indicated that the levels of transcripts changed significantly in "metabolic process", including "terpenoid biosynthetic process".These data lay the basis for elucidating the molecular mechanism of floral scent formation and regulation in monocot.

View Article: PubMed Central - PubMed

Affiliation: The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China. yueyuechong@stu.scau.edu.cn.

ABSTRACT

Background: Hedychium coronarium is a popular ornamental plant in tropical and subtropical regions because its flowers not only possess intense and inviting fragrance but also enjoy elegant shape. The fragrance results from volatile terpenes and benzenoids presented in the floral scent profile. However, in this species, even in monocots, little is known about the underlying molecular mechanism of floral scent production.

Results: Using Illumina platform, approximately 81 million high-quality reads were obtained from a pooled cDNA library. The de novo assembly resulted in a transcriptome with 65,591 unigenes, 50.90% of which were annotated using public databases. Digital gene expression (DGE) profiling analysis revealed 7,796 differential expression genes (DEGs) during petal development. GO term classification and KEGG pathway analysis indicated that the levels of transcripts changed significantly in "metabolic process", including "terpenoid biosynthetic process". Through a systematic analysis, 35 and 33 candidate genes might be involved in the biosynthesis of floral volatile terpenes and benzenoids, respectively. Among them, flower-specific HcDXS2A, HcGPPS, HcTPSs, HcCNL and HcBCMT1 might play critical roles in regulating the formation of floral fragrance through DGE profiling coupled with floral volatile profiling analyses. In vitro characterization showed that HcTPS6 was capable of generating β-farnesene as its main product. In the transcriptome, 1,741 transcription factors (TFs) were identified and 474 TFs showed differential expression during petal development. It is supposed that two R2R3-MYBs with flower-specific and developmental expression might be involved in the scent production.

Conclusions: The novel transcriptome and DGE profiling provide an important resource for functional genomics studies and give us a dynamic view of biological process during petal development in H. coronarium. These data lay the basis for elucidating the molecular mechanism of floral scent formation and regulation in monocot. The results also provide the opportunities for genetic modification of floral scent profile in Hedychium.

No MeSH data available.


Related in: MedlinePlus

Expression patterns of genes encoding enzymes possibly involved in the shikimate/benzenoid pathway in H. coronarium. The abbreviated name of enzyme in each catalytic step is showed in bold. Gene expression levels (log10 RPKM) in three developmental stages (D1: squaring stage; D4: blooming stage; D6: senescence stage) are represented by color gradation. Gene expression with RPKM ≤ 1 was set to 0 after log10 transformation. The subcellular localization of BALD in blue was predicted as mitochondria. Broken arrows represent hypothetical steps not yet described in plant. Genes with more than one homology are represented by equal colored horizontal stripe and are termed from top to bottom in Arabic numerical order. The full names of enzymes are listed in the section of “Abbreviations”
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Fig8: Expression patterns of genes encoding enzymes possibly involved in the shikimate/benzenoid pathway in H. coronarium. The abbreviated name of enzyme in each catalytic step is showed in bold. Gene expression levels (log10 RPKM) in three developmental stages (D1: squaring stage; D4: blooming stage; D6: senescence stage) are represented by color gradation. Gene expression with RPKM ≤ 1 was set to 0 after log10 transformation. The subcellular localization of BALD in blue was predicted as mitochondria. Broken arrows represent hypothetical steps not yet described in plant. Genes with more than one homology are represented by equal colored horizontal stripe and are termed from top to bottom in Arabic numerical order. The full names of enzymes are listed in the section of “Abbreviations”

Mentions: Given that the shikimate and arogenate pathways provide the carbon flux for the biosynthesis of benzenoids in plant, the genes related to shikimate and arogenate pathways were first investigated. The shikimate pathway consists of seven reactions catalyzed by six enzymes in plant and originates from phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) to produce chorismate [63]. Nine complete shikimate pathway genes were identified in the transcriptome, including two 3-deoxy-7-phosphoheptulonate synthase (DAHPS) genes, three shikimate kinase (SK) genes and one each of 3-dehydroquinate synthase (DHQS) gene, dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SHD), 3-phospho shikimate 1-carboxyvinyltransferase (EPSPS) gene and chorismate synthase (CS) gene (Fig. 8). The expression levels of these genes at three stages were showed in Fig. 8. Among them, DAHPS is the first committed enzyme in shikimate pathway and controls the overall carbon flux into the pathway [64]. The HcDAHPS1 gene displayed a very high expression level during the petal development, while the expression level of HcDAHPS2 was low, suggesting that HcDAHPS1 play a key role in regulating the carbon flux into the shikimate pathway. Following the formation of chorismate, phenylalanine was synthesized via the arogenate pathway, including three chorismate mutases (CMs), one prephenate aminotransferase (PAT) and five arogenate dehydratases (ADTs) in H. coronarium. In five ADT genes, only HcADT1 was up-regulated significantly in the process of D1 to D4, while HcADT2-4 was down-regulated. All aforementioned enzymes were predicted to be plastidial localization (Fig. 8).Fig. 8


Transcriptome profiling provides new insights into the formation of floral scent in Hedychium coronarium.

Yue Y, Yu R, Fan Y - BMC Genomics (2015)

Expression patterns of genes encoding enzymes possibly involved in the shikimate/benzenoid pathway in H. coronarium. The abbreviated name of enzyme in each catalytic step is showed in bold. Gene expression levels (log10 RPKM) in three developmental stages (D1: squaring stage; D4: blooming stage; D6: senescence stage) are represented by color gradation. Gene expression with RPKM ≤ 1 was set to 0 after log10 transformation. The subcellular localization of BALD in blue was predicted as mitochondria. Broken arrows represent hypothetical steps not yet described in plant. Genes with more than one homology are represented by equal colored horizontal stripe and are termed from top to bottom in Arabic numerical order. The full names of enzymes are listed in the section of “Abbreviations”
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4472261&req=5

Fig8: Expression patterns of genes encoding enzymes possibly involved in the shikimate/benzenoid pathway in H. coronarium. The abbreviated name of enzyme in each catalytic step is showed in bold. Gene expression levels (log10 RPKM) in three developmental stages (D1: squaring stage; D4: blooming stage; D6: senescence stage) are represented by color gradation. Gene expression with RPKM ≤ 1 was set to 0 after log10 transformation. The subcellular localization of BALD in blue was predicted as mitochondria. Broken arrows represent hypothetical steps not yet described in plant. Genes with more than one homology are represented by equal colored horizontal stripe and are termed from top to bottom in Arabic numerical order. The full names of enzymes are listed in the section of “Abbreviations”
Mentions: Given that the shikimate and arogenate pathways provide the carbon flux for the biosynthesis of benzenoids in plant, the genes related to shikimate and arogenate pathways were first investigated. The shikimate pathway consists of seven reactions catalyzed by six enzymes in plant and originates from phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) to produce chorismate [63]. Nine complete shikimate pathway genes were identified in the transcriptome, including two 3-deoxy-7-phosphoheptulonate synthase (DAHPS) genes, three shikimate kinase (SK) genes and one each of 3-dehydroquinate synthase (DHQS) gene, dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SHD), 3-phospho shikimate 1-carboxyvinyltransferase (EPSPS) gene and chorismate synthase (CS) gene (Fig. 8). The expression levels of these genes at three stages were showed in Fig. 8. Among them, DAHPS is the first committed enzyme in shikimate pathway and controls the overall carbon flux into the pathway [64]. The HcDAHPS1 gene displayed a very high expression level during the petal development, while the expression level of HcDAHPS2 was low, suggesting that HcDAHPS1 play a key role in regulating the carbon flux into the shikimate pathway. Following the formation of chorismate, phenylalanine was synthesized via the arogenate pathway, including three chorismate mutases (CMs), one prephenate aminotransferase (PAT) and five arogenate dehydratases (ADTs) in H. coronarium. In five ADT genes, only HcADT1 was up-regulated significantly in the process of D1 to D4, while HcADT2-4 was down-regulated. All aforementioned enzymes were predicted to be plastidial localization (Fig. 8).Fig. 8

Bottom Line: The de novo assembly resulted in a transcriptome with 65,591 unigenes, 50.90% of which were annotated using public databases.GO term classification and KEGG pathway analysis indicated that the levels of transcripts changed significantly in "metabolic process", including "terpenoid biosynthetic process".These data lay the basis for elucidating the molecular mechanism of floral scent formation and regulation in monocot.

View Article: PubMed Central - PubMed

Affiliation: The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China. yueyuechong@stu.scau.edu.cn.

ABSTRACT

Background: Hedychium coronarium is a popular ornamental plant in tropical and subtropical regions because its flowers not only possess intense and inviting fragrance but also enjoy elegant shape. The fragrance results from volatile terpenes and benzenoids presented in the floral scent profile. However, in this species, even in monocots, little is known about the underlying molecular mechanism of floral scent production.

Results: Using Illumina platform, approximately 81 million high-quality reads were obtained from a pooled cDNA library. The de novo assembly resulted in a transcriptome with 65,591 unigenes, 50.90% of which were annotated using public databases. Digital gene expression (DGE) profiling analysis revealed 7,796 differential expression genes (DEGs) during petal development. GO term classification and KEGG pathway analysis indicated that the levels of transcripts changed significantly in "metabolic process", including "terpenoid biosynthetic process". Through a systematic analysis, 35 and 33 candidate genes might be involved in the biosynthesis of floral volatile terpenes and benzenoids, respectively. Among them, flower-specific HcDXS2A, HcGPPS, HcTPSs, HcCNL and HcBCMT1 might play critical roles in regulating the formation of floral fragrance through DGE profiling coupled with floral volatile profiling analyses. In vitro characterization showed that HcTPS6 was capable of generating β-farnesene as its main product. In the transcriptome, 1,741 transcription factors (TFs) were identified and 474 TFs showed differential expression during petal development. It is supposed that two R2R3-MYBs with flower-specific and developmental expression might be involved in the scent production.

Conclusions: The novel transcriptome and DGE profiling provide an important resource for functional genomics studies and give us a dynamic view of biological process during petal development in H. coronarium. These data lay the basis for elucidating the molecular mechanism of floral scent formation and regulation in monocot. The results also provide the opportunities for genetic modification of floral scent profile in Hedychium.

No MeSH data available.


Related in: MedlinePlus