The inflorescence transcriptome of Orchis italica, a wild Mediterranean orchid species.

The family Orchidaceae includes more than 25,000 species known for their beauty and adaptation to different habitats. The zygomorphic flowers of orchids, extremely diversified, are organized into three outer tepals, two inner lateral tepals and one inner median tepal (lip or labellum). The column is a fusion of male and female reproductive tissues, at whose apex are located the pollen grains. At the base of the column is positioned the ovary whose maturation is triggered by pollination. Orchis italica (Orchidoideae, Orchidinae), the ???naked man orchid???, is one of the most abundant Italian wild orchids. Recently, molecular evolutionary studies have been addressed to dissect the molecular mechanisms regulating flower development in this orchid species. As the genome of O. italica (or other orchid species) is not available, we assembled and analyzed the floral transcriptome of O. italica using the Illumina RNA-seq technology and de novo assembly and analysis tools. Starting from more than 100 million raw reads, we obtained 132,565 assembled transcripts clustered in 86,079 unigenes. Functional annotation assigned 45.3% of unigenes to records present in the NCBI nr protein database, 37.4% to GO terms, 18.3% to KOG groups and 8.3% to KEGG pathways. We confirmed the in silico expression analysis by Real Time RT-PCR on 10 selected unigenes, showing high and statistically significant positive correlation. In addition to the coding transcripts, we analyzed the putative long non-coding RNAs using two different prediction software, CPC and Portrait. We examined the expression pattern of selected putative long non-coding RNAs in different tissues of O. italica, hypothesizing their possible functional role in the floral tissues.