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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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Transcriptome Sequence Analysis of an Ornamental Plant, Ananas comosus var. bracteatus, Revealed the Potential Unigenes Involved in Terpenoid and Phenylpropanoid Biosynthesis