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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.

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The Phenylpropanoid 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.g008: The Phenylpropanoid 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: As is well known, lignin plays a crucial role in plant development and prevents pathogen invasion [26]. Aside from the structural function, lignin derivatives have been shown to have several bioactive functions. Recently, Ito et al. reported that lignin derivatives suppress the apoptosis of neural cells caused by oxidative stress [27]. The initial step in its biosynthesis involves the deamination of phenylalanine to cinnamic acid by phenylalanine ammonia lyase (PAL, EC 4.3.1.24, 11 unigenes) (Fig. 8). Cinnamic is converted into ferulic and sinapic acids by trans-cinnamate 4-monooxygenase (C4H, EC 1.14.13.11, 5 unigenes), coniferyl-aldehyde dehydrogenase (REF1, EC 1.2.1.68, 8 unigenes) and ferulate 5-hydroxlase (F5H, EC 1.14.-.-, 1 unigene). These acids are then ligated to CoA, leading to the synthesis of CoA acid derivatives (caffeoyl-CoA, Feruloyl-CoA, 5-hydroxy-feruloyl-CoA and sinapoyl-CoA) by 4-coumarate-CoA ligase (4CL, EC6.2.1.12; 6 unigenes). Other intermediate enzyme, caffeoyl-CoA O-methyltransferase (CCoAMT, EC 2.1.1.104, 5 unigenes) convert caffeoyl-CoA to Feruloyl-CoA and 5-hydroxy-feruloyl-CoA to sinapoyl-CoA. Next, cinnamoyl-CoA reductase (CCR, EC1.2.1.44, 5 unigenes) converts acids into caffeoyl, Feruloyl, 5-hydroxy-feruloyl and sinapoyl aldehydes. All these aldehydes synthesized above then reduced to alcoholic compound bycinnamyl-alcohol dehydrogenase (CAD, EC: 1.1.1.195; 2 unigenes). In the final step, aldehydes are polymerized into p-Hydroxyphenyl lignin, Guaiacyl lignin, 5-Hydroxyguaiacyl lignin and syringyl lignin by peroxidase (EPO, EC 1.11.1.7, 25 unigenes). The EC number and number of unigenes encoding the enzymes involved in the phenylpropanoid biosynthesis are listed in the 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 Phenylpropanoid 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.g008: The Phenylpropanoid 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: As is well known, lignin plays a crucial role in plant development and prevents pathogen invasion [26]. Aside from the structural function, lignin derivatives have been shown to have several bioactive functions. Recently, Ito et al. reported that lignin derivatives suppress the apoptosis of neural cells caused by oxidative stress [27]. The initial step in its biosynthesis involves the deamination of phenylalanine to cinnamic acid by phenylalanine ammonia lyase (PAL, EC 4.3.1.24, 11 unigenes) (Fig. 8). Cinnamic is converted into ferulic and sinapic acids by trans-cinnamate 4-monooxygenase (C4H, EC 1.14.13.11, 5 unigenes), coniferyl-aldehyde dehydrogenase (REF1, EC 1.2.1.68, 8 unigenes) and ferulate 5-hydroxlase (F5H, EC 1.14.-.-, 1 unigene). These acids are then ligated to CoA, leading to the synthesis of CoA acid derivatives (caffeoyl-CoA, Feruloyl-CoA, 5-hydroxy-feruloyl-CoA and sinapoyl-CoA) by 4-coumarate-CoA ligase (4CL, EC6.2.1.12; 6 unigenes). Other intermediate enzyme, caffeoyl-CoA O-methyltransferase (CCoAMT, EC 2.1.1.104, 5 unigenes) convert caffeoyl-CoA to Feruloyl-CoA and 5-hydroxy-feruloyl-CoA to sinapoyl-CoA. Next, cinnamoyl-CoA reductase (CCR, EC1.2.1.44, 5 unigenes) converts acids into caffeoyl, Feruloyl, 5-hydroxy-feruloyl and sinapoyl aldehydes. All these aldehydes synthesized above then reduced to alcoholic compound bycinnamyl-alcohol dehydrogenase (CAD, EC: 1.1.1.195; 2 unigenes). In the final step, aldehydes are polymerized into p-Hydroxyphenyl lignin, Guaiacyl lignin, 5-Hydroxyguaiacyl lignin and syringyl lignin by peroxidase (EPO, EC 1.11.1.7, 25 unigenes). The EC number and number of unigenes encoding the enzymes involved in the phenylpropanoid biosynthesis are listed in the 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