ArticlePlant molecular biology2014
Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite.
Article in Plant molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
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- Genome-wide analysis of small RNAs from Odontoglossum ringspot virus and Cymbidium mosaic virus synergistically infecting Phalaenopsis.Molecular plant pathology · 2020Article
- Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms.Frontiers in genetics · 2019Article
- Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding.Plant biotechnology journal · 2018Article
- Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing.Scientific reports · 2018Article
- Post genomics era for orchid research.Botanical studies · 2017Review
- Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress.BMC plant biology · 2017Article
- Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii.BMC genomics · 2017Article
- New technologies accelerate the exploration of non-coding RNAs in horticultural plants.Horticulture research · 2017Review
- Application of a modified drop method for high-resolution pachytene chromosome spreads in two Phalaenopsis species.Molecular cytogenetics · 2016Article
- Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling.Plant cell reports · 2016Article
- DhEFL2, 3 and 4, the three EARLY FLOWERING4-like genes in a Doritaenopsis hybrid regulate floral transition.Plant cell reports · 2015Article
- Article
- Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum).Plant signaling & behavior · 2014Article
- De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts.PloS one · 2014Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.
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