An abundant LINE-like element amplified in the genome of Lilium speciosum

Abstract

The genomes of Lilium species are very large, containing 30-40 million kilobase pairs of DNA. An abundant fragment of 3.5 kb was released by BamHI digestion of genomic DNA of Lilium speciosum. Analysis of 20 genomic clones containing sequences homologous to the fragment showed it to be part of a 4.45 kb dispersed repeat, which was named del2. Sequence analysis of one full element and regions of four others revealed del2 to be a non-LTR (long terminal repeat) retrotransposon. It is flanked by short direct repeats of from 4 to 13 bp and a run of adenines occurs at one end (the proposed 3' end), 63 bp downstream from a polyadenylation signal. A possible RNA polymerase II promoter similar to that found in Drosophila I and F group elements is present internally 30 bp downstream from the 5' end. Two degenerate open reading frames (ORFs) are present, the 5' ORF containing a gag-related cysteine motif, and the 3' ORF containing a different cysteine motif also found in most non-LTR retrotransposons. The 3' ORF also has regions with homology to reverse transcriptase sequences, which are most similar to those in Cin4 of maize, the L1 LINE elements of humans and mice and the R2 ribosomal DNA inserts of insects. The majority of del2 elements occur as the full 4.45 kb element. They account for an estimated 4% of the L. speciosum genome and are present in approximately 250,000 copies. del2-related sequences were also detected in 12 other monocot species.(ABSTRACT TRUNCATED AT 250 WORDS)

Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants.

“…Some known plant retrotransposons occur at high copy number in their host genomes (Grandbastien, 1992). The de12 (dispersed element of lilies) element, for example, constitutes 4% of the lily genome (Leeton and Smyth, 1993). Previously, we have described a recent insertion of a mobile element, Tourist-Zml (zea Eays), in a maize waxy allele (Bureau and Wessler, 1992).…”

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

“…Non-LTR retroelements, such as longinterspersed nuclear elements (LINEs) and short-interspersed nuclear elements (SINEs) have also been identified in plants (Kumar and Bennetzen 1999). Abundant LINE and SINE elements, however, have not been identified in maize, although they may make up a small percentage of other plant genomes (Leeton and Smyth 1993;Yoshioka et al 1993;The Arabidopsis Genome Initiative 2000). In contrast, the repetitive fraction of the human genome comprises, for the most part, SINE and LINE elements, whereas LTR retrotransposons are less abundant (International Human Genome Sequencing Consortium 2001).…”

LINE-Like Retrotransposition inSaccharomyces cerevisiae

“…Nonsense or missense mutations within the first zinc knuckle motif of ORF1 eliminated retrotransposition activity. Although these zinc knuckle motifs are not present in mammalian ORF1, they can be found in other members of the L1 clade (SchwarzSommer et al 1987;Garrett et al 1989;Leeton and Smyth 1993;Wright et al 1996) and may represent the functional surrogate of the known RNA binding activity of human/mouse ORF1. Similarly, a reverse transcriptase missense mutation abolished retrotransposition.…”