ArticlePloS one2014
De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Modular control of orchid beauty: co-expression networks orchestrate organ development and evolution in Phalaenopsis flower.Plant molecular biology · 2026Article
- Transcriptome characterization and population genetics ofBiodiversity data journal · 2026Article
- Evolutionary dynamics of Orchid DL paralogs: gene duplication, functional divergence, and expression patterns across Orchid subfamilies.BMC plant biology · 2025Article
- Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.).Molecular ecology · 2023Article
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- Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond.Frontiers in plant science · 2022Article
- Evolution and development of three highly specialized floral structures of bee-pollinatedEvoDevo · 2020Article
- Duplication and selection in β-ketoacyl-ACP synthase gene lineages in the sexually deceptive Chiloglottis (Orchidaceace).Annals of botany · 2019Article
- Evolutionary Conservation of the Orchid MYB Transcription Factors DIV, RAD, and DRIF.Frontiers in plant science · 2019Article
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- Development of polymorphic microsatellite markers by using de novo transcriptome assembly of Calanthe masuca and C. sinica (Orchidaceae).BMC genomics · 2018Article
- Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau.Scientific reports · 2018Article
- Post genomics era for orchid research.Botanical studies · 2017Review
- Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima.Molecular ecology · 2017Article
- Transcriptome-Wide Identification and Expression Analysis of DIVARICATA- and RADIALIS-Like Genes of the Mediterranean Orchid Orchis italica.Genome biology and evolution · 2017Article
- RNA-Seq Expression Analysis of Enteric Neuron Cells with Rotenone Treatment and Prediction of Regulated Pathways.Neurochemical research · 2017Article
- De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation.PloS one · 2016Article
- Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica.Scientific reports · 2015Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The floral transcriptome of Orchis italica, a wild orchid species, was obtained using Illumina RNA-seq technology and specific de novo assembly and analysis tools. More than 100 million raw reads were processed resulting in 132,565 assembled transcripts and 86,079 unigenes with an average length of 606 bp and N50 of 956 bp. Functional annotation assigned 38,984 of the unigenes to records present in the NCBI non-redundant protein database, 32,161 of them to Gene Ontology terms, 15,775 of them to Eukaryotic Orthologous Groups (KOG) and 7,143 of them to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The in silico expression analysis based on the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was confirmed by real-time RT-PCR experiments on 10 selected unigenes, which showed high and statistically significant positive correlation with the RNA-seq based expression data. The prediction of putative long non-coding RNAs was assessed using two different software packages, CPC and Portrait, resulting in 7,779 unannotated unigenes that matched the threshold values for both of the analyses. Among the predicted long non-coding RNAs, one is the homologue of TAS3, a long non-coding RNA precursor of trans-acting small interfering RNAs (ta-siRNAs). The differential expression pattern observed for the selected putative long non-coding RNAs suggests their possible functional role in different floral tissues.
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