Delineating genome-wide alternative splicing landscapes and their functional significance in orchids

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Research Article

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South African Journal of Botany


Orchids are one of the most attractive groups of flowers with exceptional morphological diversity and high commercial value. Orchid plants are evolved to thrive in diverse habitats under different climatic conditions. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to modulate transcript diversity for necessary physiological functions in plants. Present study deals with the genome-wide AS landscapes and their functional relevance in six orchid species, information on which was inadequate so far. A total of 180 transcriptome datasets representing different tissues and treatments were chosen from the orchid taxa with well-annotated, publicly accessible genome asssemblies. Cleaned RNA-seq reads were aligned against corresponding reference genomes followed by de-novo transcriptome assembly and detection of novel AS events with significant read support. Alternative acceptor sites (A3S) and intron retentions (IR) were the most prevalent type of AS events. Under cold acclimation, exon skipping events were observed to be elevated in D. officinale leaves. Incidences of intron retentions were elevated in response to pathogen stress, that further amplified offering jasmonate mediated immunity in D. catenatum. GO enrichment of AS-affected genes suggested that most of them are functionally involved in cellular metabolism and RNA processing. A major fraction of genes could be detected that are not differentially expressed in general, however, specific splice variants of them are significantly up/down-regulated with the biotic or abiotic stress mediated responses. Functional information on the AS-affected genes and expressional dynamics of the resultant isoforms would serve as potential genomic resources for orchid research.

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