Abstract
Polianthes tuberosa is commercially popular because of their economic importance in floriculture for cut and loose flowers and in perfume industry because of the unique fragrance. Despite its commercial importance, no ready-to-use transcript sequence information is available in the public database. We have sequenced the RNA obtained from tuberose flowers using the Illumina HiSeq. 2000 platform and have carried out a de novo analysis of the transcriptome data. The de novo assembly generated 11,100 transcripts. These transcripts represent a total of 7876 unigenes that were considered for downstream analysis. These 7876 unigenes, which was further annotated using blast2go and KEGG pathways, were also assigned. Tuberose transcripts were also assigned to metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes database to determine their biochemical functions. 4591 of the tuberose transcripts matched to genes in KEGG pathways and 66 transcripts were mapped to the Flavonoid biosynthesis pathway. 21 flowering genes have been identified in this tuberose transcriptome. Transcription factor analysis helped in the identification of a large number of transcripts similar to key genes in the flowering regulation network of Arabidopsis thaliana. Among the transcription factors identified “NAC” which is associated with plant stress response represented the most abundant category followed by APETALA2 (AP2)/ethylene-responsive element binding proteins (EREBPs) which plays various role in floral organ identity and respond to different biotic and abiotic stress.
Highlights
Identification of putative flowering genes and transcription factors from flower de novo transcriptome dataset of tuberose (Polianthes tuberosa L.)
Plant Biotechnology and Bioinformatics Transcriptome Table, text file, graph, figure Illumina Hiseq. 2000 platform at SciGenom Next-Gen sequencing facility Analyzed RNA was isolated from flowers of Polianthes tuberosa Transcriptome sequence of tuberose flower and de novo analysis for identification of flowering genes and transcription factors New Delhi, India Data is with this article and the raw sequence data generated has been deposited in the SRA database for public access (BioSample accession ID: SAMN05006898)
Flowering genes and transcription factors were identified from the transcriptome data successfully
Summary
Opened tuberose flowers of cultivar Shringar were collected and were immediately frozen in liquid nitrogen and stored at À 80 °C. Total RNA was extracted from frozen flower tissues using 596 Nucleospin RNA isolation kit (Macherey-Nagel GmbH & Co. KG, Duren, Germany). Agilent 2100 Bioanalyzer (Agilent Technologies) was used to assess the quality and quantity of RNA. OligodT beads (Illuminas TruSeqs RNA Sample Preparation Kit v2) were used to purify mRNA from one microgram of total RNA. Agencourt Ampure XP SPRI beads (Beckman-Coulter) were used to clean the cDNA. Illumina adapters were ligated to the cDNA molecules after end repair and the addition of an ‘A’ base followed by SPRI clean-up. The resultant cDNA library was amplified using PCR for the enrichment of adapter-ligated fragments, quantified using a Nanodrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). The libraries were sequenced on Illumina Hiseq. The libraries were sequenced on Illumina Hiseq. 2000 platform at SciGenom Next-Gen sequencing facility, Cochin, India
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