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

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.ResultsThe 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.ConclusionThe 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.

Physiological Characterization and Comparative Transcriptome Analysis of White and Green Leaves of Ananas comosus var. bracteatus

“…The comparative analysis of the sequenced transcriptome and the reference genome [9, 17, 31] could reveal the common and unique features in the Ananas species. The CGr and CWh shoots, derived from the callus of the chimera plant, represent the normal green and albino white cells of the chimera leaves, respectively.…”

“…The raw reads were filtered and clean reads were mapped to the reference sequence database derived from Ananas [9, 17, 31]. After the removal of adaptor sequences and the exclusion of contaminated or short reads, 11 million reads each with the Cycle Q30 percentages 88.44% and 88.42% were yielded.…”

“…The high quality reads were annotated by BLAST best hit mapping to Ananas comosus var. bracteatus representative unigenes (NCBI BioProject: PRJNA317274, NCBI BioSample: SAMN04604740) [17]. Quantitative expression was determined by mapping of all Illumina reads against A .…”

De novo assembly and characterization of leaf and floral transcriptomes of the hybridizing bromeliad species (Pitcairnia spp.) adapted to Neotropical Inselbergs

“…bracteatus (Ma et al . ). To our knowledge, this is the first report of the floral transcriptome of any bromeliad species.…”

Advances in and perspectives on evolution in Bromeliaceae

“…Coppins & F.Leal] (Ming et al, 2015), complete plastid genomes of A. comosus (Nashima et al, 2015; Redwan, Saidin & Kumar, 2015) and transcriptomes of several bromeliads (Pitcairnia: Palma-Silva et al, 2016; Fosterella: W€ ohrmann et al, 2016; Aechmea: Li et al, 2015;Ananas:Ong, Voo & Kumar, 2012;Ma et al, 2015; Vriesea: Guzman et al, 2013) will also contribute greatly to evolutionary studies on this family by serving as references for new marker discovery. Schult.…”