Limits...
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

Related in: MedlinePlus

Overview of the A. comosus var. bracteatus transcriptome sequencing and assembly.(A) Length distribution of A. comosus var. bracteatus transcripts. (B) Size distribution of A. comosus var. bracteatus unigenes. (C) Log-log plot showing the dependence of unigene lengths on the number of reads assembled into each unigene.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4358926&req=5

pone.0119153.g001: Overview of the A. comosus var. bracteatus transcriptome sequencing and assembly.(A) Length distribution of A. comosus var. bracteatus transcripts. (B) Size distribution of A. comosus var. bracteatus unigenes. (C) Log-log plot showing the dependence of unigene lengths on the number of reads assembled into each unigene.

Mentions: The cDNA library for A. comosus var. bracteatus was prepared and sequenced using the Illumina Genome analyzer. In order to accurately analyze the data, we filter the raw data to ensure the quality of each reads the value of less than 20 nucleotides does not exceed 20%, N content of not more than 5% removal of ribosomal RNA. After data filtering, 23,584,613 (23.5 million) reads with 98.64% Q20 bases were selected as high quality reads for further analysis. After the removal of adaptor sequences and exclusion of contaminated or short reads, 23.5 million high quality read sequences were assembled into 1,134,553,18 contigs using SOAPdenovo [22]. Using the Trinity de novo assembly program, short-reads were assembled into 1,186,576,93 transcripts with a mean length of 1224.83 bp (Fig. 1A). The transcripts were subjected to cluster and assembly analyses. A total 41,052 unigenes were obtained, with an average length of 837.62 bp, among which 10,923 genes (26.61%) were greater than 1 kb (Fig. 1B). These results demonstrated the effectiveness of Illumina sequencing technology in rapidly capturing a large portion of the transcriptome.


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)

Overview of the A. comosus var. bracteatus transcriptome sequencing and assembly.(A) Length distribution of A. comosus var. bracteatus transcripts. (B) Size distribution of A. comosus var. bracteatus unigenes. (C) Log-log plot showing the dependence of unigene lengths on the number of reads assembled into each unigene.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0119153.g001: Overview of the A. comosus var. bracteatus transcriptome sequencing and assembly.(A) Length distribution of A. comosus var. bracteatus transcripts. (B) Size distribution of A. comosus var. bracteatus unigenes. (C) Log-log plot showing the dependence of unigene lengths on the number of reads assembled into each unigene.
Mentions: The cDNA library for A. comosus var. bracteatus was prepared and sequenced using the Illumina Genome analyzer. In order to accurately analyze the data, we filter the raw data to ensure the quality of each reads the value of less than 20 nucleotides does not exceed 20%, N content of not more than 5% removal of ribosomal RNA. After data filtering, 23,584,613 (23.5 million) reads with 98.64% Q20 bases were selected as high quality reads for further analysis. After the removal of adaptor sequences and exclusion of contaminated or short reads, 23.5 million high quality read sequences were assembled into 1,134,553,18 contigs using SOAPdenovo [22]. Using the Trinity de novo assembly program, short-reads were assembled into 1,186,576,93 transcripts with a mean length of 1224.83 bp (Fig. 1A). The transcripts were subjected to cluster and assembly analyses. A total 41,052 unigenes were obtained, with an average length of 837.62 bp, among which 10,923 genes (26.61%) were greater than 1 kb (Fig. 1B). These results demonstrated the effectiveness of Illumina sequencing technology in rapidly capturing a large portion of the transcriptome.

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
Related in: MedlinePlus