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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.


Correlation analysis of fold change values obtained from RNA-Seq and Q-PCR. RNA-Seq fold change refers to the ratios of RPKM values of D4 (D6) to D1 for selected transcripts, while Q-PCR fold change is the relative quantity of D4 (D6) normalized to expression level of D1. ** indicates a significant correlation at P < 0.01
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Fig13: Correlation analysis of fold change values obtained from RNA-Seq and Q-PCR. RNA-Seq fold change refers to the ratios of RPKM values of D4 (D6) to D1 for selected transcripts, while Q-PCR fold change is the relative quantity of D4 (D6) normalized to expression level of D1. ** indicates a significant correlation at P < 0.01

Mentions: To experimentally validate the genes expression levels during petal development, twelve unigenes related to terpene and shikimate/benzenoid biosyntheses were selected for real-time quantitative PCR (Q-PCR) analysis. The results showed that the genes expression profiles obtained by Q-PCR were largely consistent with those measured by DGE profiling (Additional file 13). Linear regression analysis revealed the fold change values of Q-PCR and RNA-Seq showed a strong positive correlation (R2 = 0.9593) at the level of P ≤ 0.01 (Fig. 13). These results demonstrate the credibility of RNA-Seq data generated in this study.Fig. 13


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

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

Correlation analysis of fold change values obtained from RNA-Seq and Q-PCR. RNA-Seq fold change refers to the ratios of RPKM values of D4 (D6) to D1 for selected transcripts, while Q-PCR fold change is the relative quantity of D4 (D6) normalized to expression level of D1. ** indicates a significant correlation at P < 0.01
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig13: Correlation analysis of fold change values obtained from RNA-Seq and Q-PCR. RNA-Seq fold change refers to the ratios of RPKM values of D4 (D6) to D1 for selected transcripts, while Q-PCR fold change is the relative quantity of D4 (D6) normalized to expression level of D1. ** indicates a significant correlation at P < 0.01
Mentions: To experimentally validate the genes expression levels during petal development, twelve unigenes related to terpene and shikimate/benzenoid biosyntheses were selected for real-time quantitative PCR (Q-PCR) analysis. The results showed that the genes expression profiles obtained by Q-PCR were largely consistent with those measured by DGE profiling (Additional file 13). Linear regression analysis revealed the fold change values of Q-PCR and RNA-Seq showed a strong positive correlation (R2 = 0.9593) at the level of P ≤ 0.01 (Fig. 13). These results demonstrate the credibility of RNA-Seq data generated in this study.Fig. 13

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.