Isolation and characterization of novelTy1-copia-like retrotransposons from lily

Abstract

Species of the genus Lilium are well known for their large genomes. Although expansion of noncoding repeated DNA is believed to account for this genome size, retroelement del Ty3-gypsy is the only one described so far in the genus Lilium. We isolated Ty1-copia elements from Lilium longiflorum and named them LIREs (lily retrotransposons). The long terminal repeats, primer binding site, and polypurine tract sequences are highly similar among the LIRE elements, indicating that they are in the same lineage. Although the protein-coding regions were highly decayed, the sequence motifs of the integrase, reverse transcriptase, and RNase H domains were identifiable as belonging to the order of Ty1-copia elements. Phylogenetic analysis and primer binding site sequences revealed that these elements belonged to the Ale lineage among the six lineages of plant Ty1-copia elements. Base substitutions in the long terminal repeats estimated that the integration times of the LIRE Ty1-copia elements were between 0.7 and 5.5 mya. In situ hybridization showed that the LIRE elements were present in all the chromosomes of L. longiflorum and L. lancifolium, but absent in centromeres, telomeres, and 45S rRNA sites in both species. The LIRE elements were present very abundantly in species of the genus Lilium, but absent in other genera of the family Liliaceae, implying that the LIRE elements might have contributed to the expansion of the genome in the genus Lilium.

Genome size evolution: patterns, mechanisms, and methodological advances

“…Repetitive noncoding DNA sequences, especially transposable elements, are considered to be one of the largest contributors to genome size variation. It is, therefore, fitting that several papers in this collection explore the role of transposable elements in genome evolution (Ågren and Wright 2011;Hertweck 2013;Janicki et al 2011;Lee et al 2013). In addition, Fattash et al (2013) review the current knowledge regarding miniature inverted repeat transposable elements (MITEs), and discuss computational advances in the discovery and analysis of MITEs.…”

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

“…LINE-like element, del-2, was isolated from Lilium speciosum and the del-2 was estimated about 4 % of the L. speciosum (Leeton and Smyth 1993). Recently, Ty1/copia elements, LIREs (lily retroelements), were isolated from Lilium longiflorum (Lee et al 2013). The LIREs were present in all Lilium species analyzed with similar copies of del-1 and they were not present beyond the genus Lilium.…”

Diverse Ty1-<i>copia</i> Retrotransposons Found in Waterlilies of the Genus <i>Nymphaea</i>

“…105 rt sequences from elements well classified in previous studies were gathered as references (Kolano et al, 2013;Lee et al, 2013;Llorens et al, 2009;Wicker and Keller, 2007) (Table S1). To classify the isolated rt sequences, each amino acid sequence was individually aligned to the reference sequences with ClustalW software for phylogenetic analyses.…”

“…The development of retrotransposon-based markers for waterlilies in the future will require nucleotide sequences of conserved domains, usually in LTRs, from families of LTR-retrotransposons in order to design primers, and different approaches using the isolated rt sequences can be used to acquire complete sequences of Ty1-copia retrotransposons from genomes of Nymphaea species which have not been reported. The rt fragments may be used as hybridization probes to screen genomic libraries for genomic fragments that contain the targeted retrotransposons as performed in Lilium longiflorum (Lee et al, 2013). Or the rt sequences may be used as the initiation site for genome walking to individually find nucleotide sequences of the desired transposons as done in Fragaria species (He et al, 2010).…”