Abstract
BackgroundTransposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure.ResultsWe combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions.ConclusionOrchid-rt1 and Gypsy1–3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.
Highlights
Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations
Identification of long terminal repeat (LTR) retrotransposons The Long Terminal Repeats (LTRs) retrotransposons were identified from several sequenced genome datasets for Phalaenopsis orchids, including BAC end sequences (BESs) [23], Roche 454, Illumina/Solexa, and assembled draft whole genome sequences [11], by using two approaches
These sequences were assembled into large contigs, LTRfinder was used to identify the full-length LTR retrotransposons, which are bordered by two identical LTRs at the time of insertion and subsequently diverged by random mutations [24]
Summary
Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The C value refers to the nuclear DNA contents of the replicated haploid genome and represents the genome size of species [2]. Formosana (hereafter called P. aphrodite), have relatively small genome sizes, with 2C values of 2.95 and 2.81 pg, equivalent to 1.6and 1.52-Gbp genome sequences [3, 4]. The scented Phalaenopsis species P. violacea and P. bellina have a large genome (Additional file 1: Fig. S1), with 2C values of 12.89 and 13.04 pg, respectively, equivalent to 6.99- and 7.07-Gbp genome sizes
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