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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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Functional annotation of assembled sequences based on gene ontology (GO) categorization.GO analysis was performed at the level two for three main categories (cellular component, molecular function and biological process).
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pone.0119153.g003: Functional annotation of assembled sequences based on gene ontology (GO) categorization.GO analysis was performed at the level two for three main categories (cellular component, molecular function and biological process).

Mentions: In addition, functions of the assembled transcripts were classified using Gene Ontology (GO). A total of 17,746 unigenes were divided into three ontologies: cellular component, molecular function and biological processes. Of these, majority of the GO terms were assigned to biological processes (47%), followed by cellular component (27%) and molecular function (26%) (Fig. 3). The biological function category mainly comprised proteins involved in metabolic, cellular processes and response to stimuli, biological regulation and localization and biogenesis are most represented functions. Of these, genes involved in the metabolic and cellular processes were highly represented. In cellular components, the major classifications of these genes products were cell, cell part, organelle and membrane. For molecular functions, the genes involved in catalytic and binding activities were both highly represented. In comparison to pineapple fruit GO annotation [17], more number of the genes were expressed in all the three ontologies (cellular component, molecular function, biological function). GO annotation provided a general gene expression profile picture for A. comosus var. bracteatus, which showed that the sequenced genes were responsible for fundamental, biological regulation and metabolism.


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)

Functional annotation of assembled sequences based on gene ontology (GO) categorization.GO analysis was performed at the level two for three main categories (cellular component, molecular function and biological process).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0119153.g003: Functional annotation of assembled sequences based on gene ontology (GO) categorization.GO analysis was performed at the level two for three main categories (cellular component, molecular function and biological process).
Mentions: In addition, functions of the assembled transcripts were classified using Gene Ontology (GO). A total of 17,746 unigenes were divided into three ontologies: cellular component, molecular function and biological processes. Of these, majority of the GO terms were assigned to biological processes (47%), followed by cellular component (27%) and molecular function (26%) (Fig. 3). The biological function category mainly comprised proteins involved in metabolic, cellular processes and response to stimuli, biological regulation and localization and biogenesis are most represented functions. Of these, genes involved in the metabolic and cellular processes were highly represented. In cellular components, the major classifications of these genes products were cell, cell part, organelle and membrane. For molecular functions, the genes involved in catalytic and binding activities were both highly represented. In comparison to pineapple fruit GO annotation [17], more number of the genes were expressed in all the three ontologies (cellular component, molecular function, biological function). GO annotation provided a general gene expression profile picture for A. comosus var. bracteatus, which showed that the sequenced genes were responsible for fundamental, biological regulation and metabolism.

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