Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0150-0) contains supplementary material, which is available to authorized users.

Orchidstra 2.0—A Transcriptomics Resource for the Orchid Family

“…Moreover, we have added RNA-Seq based gene expression data for 65 tissues/developmental stages. For the pre-existing orchid miRNA (Chao et al 2014) and microarray information (Su et al 2013b), all of the newly generated RNA-Seq transcriptome data were integrated and consistency was ensured. The orchid species and tissues were selected to cover the evolutionary classification of orchids and to be relevant to orchid breeders and researchers.…”

“…Orchid genomes are typically larger than those of most model plants and there is remarkable variability in genome size across the family, with the amount of nuclear DNA varying up to 168-fold (Leitch et al 2009). Most of the effort in sequencing orchid species is being made using transcriptome sequencing (Su et al 2011, Tsai et al 2013, Zhang et al 2013, Chao et al 2014.…”

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

“…An integrated database, Orchidstra, has recently been constructed (http://orchidstra.abrc.sinica.edu.tw/; Su et al, 2013a). The Orchidstra database contains transcriptome information for five orchid species and one commercial hybrid as well as microRNA (Chao et al, 2014) and microarray-based expression profiling data for a potential orchid model species, P. aphrodite (Su et al, 2013b). Transcriptome analysis of Cymbidium using Illumina sequencing has been reported from China Zhang et al, 2013b).…”

Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum)

“…48 miR5021 was also reported in a few plant species such as peach, ginseng, sunflower, radish, longan, Jatropha curcas, moth orchid, Brassica oleracea, and Arabidopsis. 24,26,[49][50][51][52][53][54] It was indicated that miR5021 families may be involved in the regulation of lipid metabolism and responses to stress, and MYB proteins and SPL3 transcription factor may be the target of miR5021. 26 Although miR156-3p, miR1522, miR5658, miR5783, and miR5998 were also identified in other species, their functional roles remain unknown as yet.…”