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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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A. comosus var. bracteatus unigene similarity comparison with rice, maize, sorghum and Arabidopsis and functional classification by GO analysis.(A) Similarity search of A. comosus var. bracteatus sequence against rice, maize, sorghum and Arabidopsis. (B) Functional classification of A. comosus var. bracteatus unigenes with and without homologs with rice, maize, sorghum and Arabidopsis.
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pone.0119153.g006: A. comosus var. bracteatus unigene similarity comparison with rice, maize, sorghum and Arabidopsis and functional classification by GO analysis.(A) Similarity search of A. comosus var. bracteatus sequence against rice, maize, sorghum and Arabidopsis. (B) Functional classification of A. comosus var. bracteatus unigenes with and without homologs with rice, maize, sorghum and Arabidopsis.

Mentions: To study the sequence conservation of A. comosus var. bracteatus unigenes in other plant species, a BLASTX search was performed against the four available proteomes of completely sequenced plant genomes. The largest number of A. comosus var. bracteatus unigenes exhibited 22,194 significant similarity hits to rice transcript, 21,886 unigenes had similarity hits to maize, 22,183 unigenes had similarity hits to sorghum and 21,537 unigenes had similarity hits to Arabidopsis (Fig. 6A). Based on the above similarity search, we then conducted GO analysis to compare the functional classification between A. comosus var. bracteatus and the above five species (Fig. 6B). The detailed results were listed in S4 Table. A total of 20,716 shared homologues among these four species. Of these, genes involved in metabolic and cellular processes are highly represented in biological processes. Under the molecular function ontology, proteins involved in binding and catalytic activity was dominant while in cellular component ontology, proteins for cell part, cell and organelle development were generally encoded by A. comosus var. bracteatus unigenes. Therefore, we conclude that the differences in the expression profile and functional allocation of the A. comosus var. bracteatus unigenes with sequence similarity hits to four species concurrently contribute to the divergence of A. comosus var. bracteatus from other crops.


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)

A. comosus var. bracteatus unigene similarity comparison with rice, maize, sorghum and Arabidopsis and functional classification by GO analysis.(A) Similarity search of A. comosus var. bracteatus sequence against rice, maize, sorghum and Arabidopsis. (B) Functional classification of A. comosus var. bracteatus unigenes with and without homologs with rice, maize, sorghum and Arabidopsis.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0119153.g006: A. comosus var. bracteatus unigene similarity comparison with rice, maize, sorghum and Arabidopsis and functional classification by GO analysis.(A) Similarity search of A. comosus var. bracteatus sequence against rice, maize, sorghum and Arabidopsis. (B) Functional classification of A. comosus var. bracteatus unigenes with and without homologs with rice, maize, sorghum and Arabidopsis.
Mentions: To study the sequence conservation of A. comosus var. bracteatus unigenes in other plant species, a BLASTX search was performed against the four available proteomes of completely sequenced plant genomes. The largest number of A. comosus var. bracteatus unigenes exhibited 22,194 significant similarity hits to rice transcript, 21,886 unigenes had similarity hits to maize, 22,183 unigenes had similarity hits to sorghum and 21,537 unigenes had similarity hits to Arabidopsis (Fig. 6A). Based on the above similarity search, we then conducted GO analysis to compare the functional classification between A. comosus var. bracteatus and the above five species (Fig. 6B). The detailed results were listed in S4 Table. A total of 20,716 shared homologues among these four species. Of these, genes involved in metabolic and cellular processes are highly represented in biological processes. Under the molecular function ontology, proteins involved in binding and catalytic activity was dominant while in cellular component ontology, proteins for cell part, cell and organelle development were generally encoded by A. comosus var. bracteatus unigenes. Therefore, we conclude that the differences in the expression profile and functional allocation of the A. comosus var. bracteatus unigenes with sequence similarity hits to four species concurrently contribute to the divergence of A. comosus var. bracteatus from other crops.

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