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Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

Ma J, Kanakala S, He Y, Zhang J, Zhong X - PLoS ONE (2015)

Bottom Line: The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum.Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique.Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

View Article: PubMed Central - PubMed

Affiliation: College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China.

ABSTRACT

Background: Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies.

Results: The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis.

Conclusion: The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

Show MeSH
The Flavonoid biosynthesis.The A. comosus var. bracteatus transcripts encoding enzymes (highlighted) involved in the pathway was identified by BLASTx (E-value of less than 10-5). Numbers in bracket are the total number of unigenes encode for the enzyme.
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pone.0119153.g009: The Flavonoid biosynthesis.The A. comosus var. bracteatus transcripts encoding enzymes (highlighted) involved in the pathway was identified by BLASTx (E-value of less than 10-5). Numbers in bracket are the total number of unigenes encode for the enzyme.

Mentions: Unigenes involved in the flavonoid biosynthesis were also present in A. comosus var. bracteatus transcriptome dataset. Flavoniods, are a class of plant secondary metabolites, play a vital biological and pharmacological activities in in vitro studies [28]. The flavonoid biosynthetic pathways have already have been reported in snapdragon (Antirrhinum majus), petunia (Petunia hybrida) A. thaliana, Z. mays and V. vinifera [29,30]. Flavonoids are synthesized via the phenylpropanoid pathway, where the phenylalanine is used to produce 4-coumaryol-CoA, and this then combined with malonyl-CoA to produce chalcones which are backbones of flavonoids (Fig. 9). The first step involves the activity of four enzymes, phenylalanine ammonia lyase (PAL, EC 4.3.1.24, 11 unigenes), cinnamate 4-hydroxylase (C4H, EC 1.14.13.11, 5 unigenes), 4- coumarate CoA ligase (4CL, EC 6.2.1.12, 6 unigenes), and chalcone synthase (CHS, EC 2.3.1.74, 1 unigene), which converts phenylalanine to chalcone. Chalcone isomerase (CHI, EC 5.5.1.6, 1 unigene) then catalyzes the isomerisation of chalcones into naringenin. Subsequently, Naringenin is converted into flavonones, eriodictyol and dihydrotricetin by two enzymes namely, flavonoid 3’- hydroxylase (F3’H, EC 1.14.13.21, 1 unigene) and flavonoid 3’, 5’-hydroxylase (F3’5’H, EC 1.14.13.88, 2 unigenes) respectively. Flavanone 3-hydroxylase (F3H, EC 1.14.11.9) which converts flavanones to dihydroflavonols was not detected in annotated unigenes. Dihydroflavonols can then lead to production of flavonols and flavan—3, 4-diols (leucoanthocyanidin), reactions being catalysed by flavonol synthase (FLS, EC 1.14.11.23, 1unigene) and by dihydroflavonol 4-reductase (DFR, EC 1.1.1.219, 2 unigenes) respectively. The leucoanthocyanidins can either be converted to anthocyanidins by leucoanthocyanidin dioxygenase (ANS, EC 1.14.11.19, 1 unigene). We also failed to find any Anthocyanidin reductase (LAR, EC 1.17.1.3) which is responsible for production of catechins, however, we did identify one leucoanthocyanidin dioxygenase (ANS), suggesting that the genes encoding other anthocyanidine-related products may exist but have not yet been identified in the A. comosus var. bracteatus. The Anthocyanin and flavones formed here are important pigments for the beautiful red color of the leaf and fruit of A. comosus var. bracteatus. Unigenes of A. comosus var. bracteatus encoding twelve enzymes in the flavonone biosynthesis pathway are listed in S5 Table.


Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

Ma J, Kanakala S, He Y, Zhang J, Zhong X - PLoS ONE (2015)

The Flavonoid biosynthesis.The A. comosus var. bracteatus transcripts encoding enzymes (highlighted) involved in the pathway was identified by BLASTx (E-value of less than 10-5). Numbers in bracket are the total number of unigenes encode for the enzyme.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358926&req=5

pone.0119153.g009: The Flavonoid biosynthesis.The A. comosus var. bracteatus transcripts encoding enzymes (highlighted) involved in the pathway was identified by BLASTx (E-value of less than 10-5). Numbers in bracket are the total number of unigenes encode for the enzyme.
Mentions: Unigenes involved in the flavonoid biosynthesis were also present in A. comosus var. bracteatus transcriptome dataset. Flavoniods, are a class of plant secondary metabolites, play a vital biological and pharmacological activities in in vitro studies [28]. The flavonoid biosynthetic pathways have already have been reported in snapdragon (Antirrhinum majus), petunia (Petunia hybrida) A. thaliana, Z. mays and V. vinifera [29,30]. Flavonoids are synthesized via the phenylpropanoid pathway, where the phenylalanine is used to produce 4-coumaryol-CoA, and this then combined with malonyl-CoA to produce chalcones which are backbones of flavonoids (Fig. 9). The first step involves the activity of four enzymes, phenylalanine ammonia lyase (PAL, EC 4.3.1.24, 11 unigenes), cinnamate 4-hydroxylase (C4H, EC 1.14.13.11, 5 unigenes), 4- coumarate CoA ligase (4CL, EC 6.2.1.12, 6 unigenes), and chalcone synthase (CHS, EC 2.3.1.74, 1 unigene), which converts phenylalanine to chalcone. Chalcone isomerase (CHI, EC 5.5.1.6, 1 unigene) then catalyzes the isomerisation of chalcones into naringenin. Subsequently, Naringenin is converted into flavonones, eriodictyol and dihydrotricetin by two enzymes namely, flavonoid 3’- hydroxylase (F3’H, EC 1.14.13.21, 1 unigene) and flavonoid 3’, 5’-hydroxylase (F3’5’H, EC 1.14.13.88, 2 unigenes) respectively. Flavanone 3-hydroxylase (F3H, EC 1.14.11.9) which converts flavanones to dihydroflavonols was not detected in annotated unigenes. Dihydroflavonols can then lead to production of flavonols and flavan—3, 4-diols (leucoanthocyanidin), reactions being catalysed by flavonol synthase (FLS, EC 1.14.11.23, 1unigene) and by dihydroflavonol 4-reductase (DFR, EC 1.1.1.219, 2 unigenes) respectively. The leucoanthocyanidins can either be converted to anthocyanidins by leucoanthocyanidin dioxygenase (ANS, EC 1.14.11.19, 1 unigene). We also failed to find any Anthocyanidin reductase (LAR, EC 1.17.1.3) which is responsible for production of catechins, however, we did identify one leucoanthocyanidin dioxygenase (ANS), suggesting that the genes encoding other anthocyanidine-related products may exist but have not yet been identified in the A. comosus var. bracteatus. The Anthocyanin and flavones formed here are important pigments for the beautiful red color of the leaf and fruit of A. comosus var. bracteatus. Unigenes of A. comosus var. bracteatus encoding twelve enzymes in the flavonone biosynthesis pathway are listed in S5 Table.

Bottom Line: The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum.Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique.Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

View Article: PubMed Central - PubMed

Affiliation: College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China.

ABSTRACT

Background: Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies.

Results: The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis.

Conclusion: The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

Show MeSH