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Background  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. However, somaclonal variations occur during micropropagation.    Results  We 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.    Conclusion  A  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.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5420-4) contains supplementary material, which is available to authorized users.

PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids