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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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Clusters of orthologous groups (COG) classification.In total, 8,505 of the 41,052 sequences with Nr hits were grouped into 25 COG classifications.
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pone.0119153.g004: Clusters of orthologous groups (COG) classification.In total, 8,505 of the 41,052 sequences with Nr hits were grouped into 25 COG classifications.

Mentions: Based on the Nr annotation, all unigenes were subjected to a search against the COG database for functional prediction and classification. In total, 8,505 unigenes with hits in Nr database could be assigned to COG classification and divided in to 25 specific categories, listed in Fig. 4. The cluster for general function prediction (17.82%) represented the largest group, followed by translation, ribosomal structure and biogenesis (10.87%), replication, recombination and repair (8.54%) and transcription (8.33%), posttranslational modification, protein turnover, chaperones (7.05%) and signal transduction mechanisms (6.94%). Approximately 5% unigenes hit with energy production and conversion, carbohydrate transport and metabolism and amino acid transport and metabolism. However, unigenes involved in secondary metabolite biosynthesis were found in the categories of energy production and conversion and secondary metabolites biosynthesis, transport and catabolism respectively.


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)

Clusters of orthologous groups (COG) classification.In total, 8,505 of the 41,052 sequences with Nr hits were grouped into 25 COG classifications.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0119153.g004: Clusters of orthologous groups (COG) classification.In total, 8,505 of the 41,052 sequences with Nr hits were grouped into 25 COG classifications.
Mentions: Based on the Nr annotation, all unigenes were subjected to a search against the COG database for functional prediction and classification. In total, 8,505 unigenes with hits in Nr database could be assigned to COG classification and divided in to 25 specific categories, listed in Fig. 4. The cluster for general function prediction (17.82%) represented the largest group, followed by translation, ribosomal structure and biogenesis (10.87%), replication, recombination and repair (8.54%) and transcription (8.33%), posttranslational modification, protein turnover, chaperones (7.05%) and signal transduction mechanisms (6.94%). Approximately 5% unigenes hit with energy production and conversion, carbohydrate transport and metabolism and amino acid transport and metabolism. However, unigenes involved in secondary metabolite biosynthesis were found in the categories of energy production and conversion and secondary metabolites biosynthesis, transport and catabolism respectively.

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