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Abstract
BackgroundOrchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation.ResultsWe isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced.ConclusionA PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.
Highlights
Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination
We successfully identified an active transposable elements (TEs), P. equestris PIF1 (PePIF1), in a Phalaenopsis genome by combining microarray data with in silico analysis and transposon display experiments
Transcriptional activation of Phalaenopsis TEs during protocorm-like bodies (PLBs) micropropagation We searched for enhanced expression of transposon- or retrotransposon-like elements from microarray data for various PLB generations of KHM487 (Fig. 1a, b)
Summary
Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. The capsules contain hundreds of thousands of dust-like seeds that germinate and produce colorless protocorms by symbiosis with fungi in nature. Hsu et al BMC Genomics (2019) 20:25 of adventitious buds or induction of protocorm-like bodies (PLBs) from callus are the two major approaches. Mass propagation produces plantlets with uniform growth and flowering time and eases the management of the orchid nursery. Among the thousands of plantlets, some mutant phenotypes due to somaclonal variation are found during the vegetative or reproductive stage [7]. Orchid growers usually use induction of PLBs or multiplication of adventitious buds with fewer than three generations to avoid a high rate of somaclonal variation
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