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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.


Phylogenetic analysis of AAEs and BCMTs in H. coronarium. a Phylogenetic tree of clade VI AAEs based on the neighbor-joining method. CNL orthologs are shadowed in grey. b Phylogenetic tree of HcBCMTs with other functional characterized plant benzenoid carboxyl methyltransferases (BCMTs). Proteins identified from H. coronarium are in bold. The scale bar indicates 5 % sequence divergence. GenBank accession numbers are shown in parentheses. The numbers at each branch indicate bootstrap percentages from 1000 replicates. At, Arabidopsis thaliana; Am, Antirrhinum majus; Cb, Clarkia breweri; Na, Nicotiana alata; Ns, Nicotiana suaveolens; Os, Oryza sativa; Ph, Petunia hybrid; Sb, Sorghum bicolor; Sf, Stephanotis floribunda; Sl, Solanum lycopersium; Zm, Zea mays
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Fig9: Phylogenetic analysis of AAEs and BCMTs in H. coronarium. a Phylogenetic tree of clade VI AAEs based on the neighbor-joining method. CNL orthologs are shadowed in grey. b Phylogenetic tree of HcBCMTs with other functional characterized plant benzenoid carboxyl methyltransferases (BCMTs). Proteins identified from H. coronarium are in bold. The scale bar indicates 5 % sequence divergence. GenBank accession numbers are shown in parentheses. The numbers at each branch indicate bootstrap percentages from 1000 replicates. At, Arabidopsis thaliana; Am, Antirrhinum majus; Cb, Clarkia breweri; Na, Nicotiana alata; Ns, Nicotiana suaveolens; Os, Oryza sativa; Ph, Petunia hybrid; Sb, Sorghum bicolor; Sf, Stephanotis floribunda; Sl, Solanum lycopersium; Zm, Zea mays

Mentions: To further analyze the process of benzenoid biosynthesis in H. coronarium, and to identify the committed genes in the pathway, the putative genes encoding enzymes involved in the benzenoid biosynthesis were sought using the local TBLASTX search. The first committed step in benzenoid biosynthesis is catalyzed by PAL, which deaminates phenylalanine to cinnamic acid [21]. One PAL gene existed in the current assembled transcriptome and its expression was significantly regulated by petal development (Fig. 8). Then, the formation of benzenoids from cinnamic acid proceeds via β-oxidative pathway and non β-oxidative pathway [22]. The β-oxidative pathway in petunia flowers needs four reactions catalyzed by three enzymes, including Cinnamate:CoA ligase/acyl-activating enzyme (CNL/AAE), cinnamoyl-CoA hydratase-dehydrogenase (CHD) and 3-ketoacyl CoA thiolase (KAT) [23–26]. Using characterized petunia genes to BLASTX search the H. coronarium transcriptome, four CNL/AAEs, three CHDs and two KATs were found. The superfamily AAE comprises carboxyl-CoA ligases and related protein in plant, and contains seven phylogenetic clades [65]. Phylogenetic analysis of the clade VI AAEs revealed that only one out of four H. coronarium AAEs, HcCNL, fell into the group of PhCNL orthologs [23] and was closely related to CNLs in other monocots (Fig. 9a). The expression pattern of HcCNL showed positive correlation with the emission of methyl benzoate (Fig. 1g and Fig. 8). For HcCHDs, the expression levels of HcCHD1 and HcCHD2 were significantly up-regulated from D1 to D4 stage, whereas HcCHD3 is constitutively expressed at three stages (Fig. 8). The expression of HcKAT1 escalated slightly from D1 to D6 stage, while HcKAT2 showed insignificant change (Fig. 8). Besides, two peroxisomal ATP-binding cassette transporters (PXAs), homologs of Arabidopsis CTS/PXA1 [27], were identified and might account for the transport of cinnamic acid into peroxisome in H. coronarium. To non-β-oxidative pathway, NAD-dependent benzaldehyde dehydrogenase (BALD) accounted for the oxidation of benzaldehyde into benzoic acid [28]. Two BALD homologs in H. coronarium were searched using the characterized snapdragon BALD gene as query sequence [28]. Different from snapdragon BALD, HcBALDs did not show correlation with the emission of benzenoids (Fig. 8).Fig. 9


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

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

Phylogenetic analysis of AAEs and BCMTs in H. coronarium. a Phylogenetic tree of clade VI AAEs based on the neighbor-joining method. CNL orthologs are shadowed in grey. b Phylogenetic tree of HcBCMTs with other functional characterized plant benzenoid carboxyl methyltransferases (BCMTs). Proteins identified from H. coronarium are in bold. The scale bar indicates 5 % sequence divergence. GenBank accession numbers are shown in parentheses. The numbers at each branch indicate bootstrap percentages from 1000 replicates. At, Arabidopsis thaliana; Am, Antirrhinum majus; Cb, Clarkia breweri; Na, Nicotiana alata; Ns, Nicotiana suaveolens; Os, Oryza sativa; Ph, Petunia hybrid; Sb, Sorghum bicolor; Sf, Stephanotis floribunda; Sl, Solanum lycopersium; Zm, Zea mays
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig9: Phylogenetic analysis of AAEs and BCMTs in H. coronarium. a Phylogenetic tree of clade VI AAEs based on the neighbor-joining method. CNL orthologs are shadowed in grey. b Phylogenetic tree of HcBCMTs with other functional characterized plant benzenoid carboxyl methyltransferases (BCMTs). Proteins identified from H. coronarium are in bold. The scale bar indicates 5 % sequence divergence. GenBank accession numbers are shown in parentheses. The numbers at each branch indicate bootstrap percentages from 1000 replicates. At, Arabidopsis thaliana; Am, Antirrhinum majus; Cb, Clarkia breweri; Na, Nicotiana alata; Ns, Nicotiana suaveolens; Os, Oryza sativa; Ph, Petunia hybrid; Sb, Sorghum bicolor; Sf, Stephanotis floribunda; Sl, Solanum lycopersium; Zm, Zea mays
Mentions: To further analyze the process of benzenoid biosynthesis in H. coronarium, and to identify the committed genes in the pathway, the putative genes encoding enzymes involved in the benzenoid biosynthesis were sought using the local TBLASTX search. The first committed step in benzenoid biosynthesis is catalyzed by PAL, which deaminates phenylalanine to cinnamic acid [21]. One PAL gene existed in the current assembled transcriptome and its expression was significantly regulated by petal development (Fig. 8). Then, the formation of benzenoids from cinnamic acid proceeds via β-oxidative pathway and non β-oxidative pathway [22]. The β-oxidative pathway in petunia flowers needs four reactions catalyzed by three enzymes, including Cinnamate:CoA ligase/acyl-activating enzyme (CNL/AAE), cinnamoyl-CoA hydratase-dehydrogenase (CHD) and 3-ketoacyl CoA thiolase (KAT) [23–26]. Using characterized petunia genes to BLASTX search the H. coronarium transcriptome, four CNL/AAEs, three CHDs and two KATs were found. The superfamily AAE comprises carboxyl-CoA ligases and related protein in plant, and contains seven phylogenetic clades [65]. Phylogenetic analysis of the clade VI AAEs revealed that only one out of four H. coronarium AAEs, HcCNL, fell into the group of PhCNL orthologs [23] and was closely related to CNLs in other monocots (Fig. 9a). The expression pattern of HcCNL showed positive correlation with the emission of methyl benzoate (Fig. 1g and Fig. 8). For HcCHDs, the expression levels of HcCHD1 and HcCHD2 were significantly up-regulated from D1 to D4 stage, whereas HcCHD3 is constitutively expressed at three stages (Fig. 8). The expression of HcKAT1 escalated slightly from D1 to D6 stage, while HcKAT2 showed insignificant change (Fig. 8). Besides, two peroxisomal ATP-binding cassette transporters (PXAs), homologs of Arabidopsis CTS/PXA1 [27], were identified and might account for the transport of cinnamic acid into peroxisome in H. coronarium. To non-β-oxidative pathway, NAD-dependent benzaldehyde dehydrogenase (BALD) accounted for the oxidation of benzaldehyde into benzoic acid [28]. Two BALD homologs in H. coronarium were searched using the characterized snapdragon BALD gene as query sequence [28]. Different from snapdragon BALD, HcBALDs did not show correlation with the emission of benzenoids (Fig. 8).Fig. 9

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.