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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5420-4) contains supplementary material, which is available to authorized users.

An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

“…[156] have been associated undesirable characteristics observed in some plantlets with the identification of somaclonal variants from PLBs, which can be morphologically identified even at the shoot bud regeneration and in vitro plantlet production stage. According to [157], the occurrence of SV in the IPR-PLBs technique is higher than that observed from adventitious bud propagation, and that most commercial laboratories use a maximum of three generations of PLBs subcultures to avoid high frequencies of somaclonal variations in this type of propagation.…”

“…Ref. [157] isolated two most expressed transposable elements and identified a new Instability Factor (PIF)-like, one of which, called PePIF1 was identified by similarity to the Phalaenopsis equestris genome sequence, and which was transposed in the somaclonal variants of cultivars of Phalaenopsis from micropropagation, which resulted in the insertion of new genes identified and sequenced by the authors.…”

Expansion of MIR482/2118 by a class‐II transposable element in cotton

“…We believe that the total number of GosTE members is underestimated based on the observation that some orthologues of the candidate autonomous elements were not identified as GosTE members because of the use of the criterion for TIRs being identical to those found in GosTE1-GosTE46. The GosTE family belongs to the PIF/Harbinger superfamily with a 3-bp TSD (Table S3) that has been reported in several plant species, but no member of this superfamily has been previously shown to be involved in MIRNA proliferation (Zhang et al, 2001(Zhang et al, , 2004Jiang et al, 2003;Grzebelus et al, 2007;Markova and Mason-Gamer, 2015;Hsu et al, 2019). GosTEs seem to be more active in the D and Dt (sub)genomes than in the A and At (sub)genomes (Table 1).…”

“…The GosTE family belongs to the PIF/Harbinger superfamily with a 3‐bp TSD (Table S3) that has been reported in several plant species, but no member of this superfamily has been previously shown to be involved in MIRNA proliferation (Zhang et al ., 2001, 2004; Jiang et al ., 2003; Grzebelus et al ., 2007; Markova and Mason‐Gamer, 2015; Hsu et al ., 2019). GosTEs seem to be more active in the D and Dt (sub)genomes than in the A and At (sub)genomes (Table 1).…”

OrchidBase 4.0: a database for orchid genomics and molecular biology

“…The addition and integration of orchid whole genomic sequences with detailed annotation information and easy-to-use web interfaces in OrchidBase 4.0 allow users to efficiently find target genes, such as floral development-related genes [ 24 ], floral pigmentation pattern-related genes [ 25 ], TCP transcription factor genes [ 11 ], and transposable element [ 26 ]. In addition, the orchid genome sequence has been supplied valuable information for plant genome evolution and comparative genomic studies [ 15 , 27 ].…”