ArticleBMC genomics2011
Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 54 citations in OpenAlex.
- Transcriptome Analysis Reveals Endogenous Hormone Changes during Spike Development inInternational journal of molecular sciences · 2022Article
- A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach.Frontiers in plant science · 2022Review
- LED Lighting - Modification of Growth, Metabolism, Yield and Flour Composition in Wheat by Spectral Quality and Intensity.Frontiers in plant science · 2018Article
- Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants.Breeding science · 2018Review
- Post genomics era for orchid research.Botanical studies · 2017Review
- De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris.Scientific data · 2016Article
- Article
- DhEFL2, 3 and 4, the three EARLY FLOWERING4-like genes in a Doritaenopsis hybrid regulate floral transition.Plant cell reports · 2015Article
- A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development.PloS one · 2015Article
- Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing.PloS one · 2015Article
- RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae).PloS one · 2015Article
- Article
- Eugenol synthase genes in floral scent variation in Gymnadenia species.Functional & integrative genomics · 2014Article
- Engineering crassulacean acid metabolism to improve water-use efficiency.Trends in plant science · 2014Review
- Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid.International journal of molecular sciences · 2014Article
- EST sequencing and gene expression profiling in Scutellaria baicalensis.EXCLI journal · 2014Article
- Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss.Extremophiles : life under extreme conditions · 2013Article
- A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.BMC genomics · 2013Article
- Next generation sequencing in predicting gene function in podophyllotoxin biosynthesis.The Journal of biological chemistry · 2013Article
- Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOrchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome.
resultsTo maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified.
conclusionPyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies.
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