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.
Highlights
Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants
The unigene set was compared to the expressed sequence tags (ESTs) derived from P. equestris [11] and P. bellina [12]
With the whole genome sequencing of P. equestris in progress, this collection of ESTs is a valuable resource that will be immediately useful for researchers, allowing for correction of assemblies, annotation, and construction of gene models to establish accurate exon-intron boundaries
Summary
Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. Like all other living organisms, present-day orchids have evolved from ancestral forms as a result of selection pressure and adaptation. They show a wide diversity of epiphytic and terrestrial growth forms and have successfully colonized almost every habitat on earth. The authors showed that the most recent common ancestor of extant orchids lived in the late Cretaceous (76-84 Mya) [7]. They suggested that Epidendroideae and Orchidoideae, two of the largest orchid subfamilies, which together represent > 95% of living orchid species, began to diversify early in the Tertiary (65 Mya) [7]
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