Genomic demography: a life-history analysis of transposable element evolution

Promislow, Daniel E. L.; Jordan, I. King; McDonald, Jared

doi:10.1098/rspb.1999.0815

Cited by 32 publications

(36 citation statements)

References 31 publications

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“…As shown in our results, the age of the full-length LTR retrotransposons in the D. melanogaster genome is substantially younger than the melanogaster species itself. Interestingly, the average ages of all fulllength LTR retrotransposons in yeast (<100,000 yr) (Promislow et al 1999) and nematode (<500,000 yr) (N. Bowen, unpubl. ) are also much younger than the age of the species in which they are contained.…”

Section: Discussionmentioning

confidence: 99%

“…Previously, LTR nucleotide identity has been used to estimate the time of insertion of LTR retrotransposons from S. cerevisiae, Zea mays, and humans. For example, the age of the Ty1 and Ty2 elements from S. cerevisiae has been estimated to be <100,000 years old (Jordan and McDonald 1999b;Promislow et al 1999). In contrast, it has been reported that the LTR retrotransposons within the ADH-region of the maize genome are much older, having transposed in the past 2 to 6 million years (SanMiguel et al 1998).…”

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confidence: 99%

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Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Bowen¹,

McDonald²

2001

Genome Res.

149

143

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The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities Ն99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 ±89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 ± .3 million years ago.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Bowen¹,

McDonald²

2001

Genome Res.

149

143

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“…LTR-LTR recombination has been measured for the Ty1-induced promoter mutation his4-912, and occurs at a rate of about 3 × 10 -6 per generation (Winston et al, 1984). Promislow et al (1999) have developed a novel "genomic demography" model to estimate long-term retrotransposition and LTR-LTR recombination rates for Ty1, Ty2, and Ty1/2 hybrid families and how long ago these elements entered the yeast genome. The computational approach resulted in similar Ty retrotransposition and loss rates of 8.67 × 10 -8 and 7.17 × 10 -8 per generation, respectively, which are much lower than those obtained experimentally.…”

Section: Ty Copy Numbermentioning

confidence: 99%

Genome evolution mediated by Ty elements in <i>Saccharomyces</i>

2005

Cytogenet Genome Res

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How mobile genetic elements molded eukaryotic genomes is a key evolutionary question that gained wider popularity when mobile DNA sequences were shown to comprise about half of the human genome. Although Saccharomyces cerevisiae does not suffer such “genome obesity”, five families of LTR-retrotransposons, Ty1, Ty2, Ty3, Ty4, and Ty5 elements, comprise about 3% of its genome. The availability of complete genome sequences from several Saccharomyces species, including members of the closely related sensu stricto group, present new opportunities for analyzing molecular mechanisms for chromosome evolution, speciation, and reproductive isolation. In this review I present key experiments from both the pre- and current genomic sequencing eras suggesting how Ty elements mediate genome evolution.

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“…The levels of Ty1AS RNA and mRNA varied between the repopulated S. paradoxus strain and S. cerevisiae, suggesting that expression levels may be species or element-specific. Our results show that genomic Ty1AS RNAs are produced in a copy-dependent manner in two different genomic environments; a repopulated genome containing essentially identical copies of recent Ty1-H3 transposition events (15), and a S. cerevisiae strain whose natural history with respect to Ty1 is more complex (22)(23)(24).Ty1 transposition at preferred integration targets was determined using a qualitative PCR-based assay in strains with different Ty1 copy numbers (Fig. S1B).…”

mentioning

confidence: 99%

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

Matsuda

Garfinkel

2009

Proc. Natl. Acad. Sci. U.S.A.

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Transposable elements impact genome function by altering gene expression and causing chromosome rearrangements. As a result, organisms have evolved mechanisms, such as RNA-interference, to minimize the level of transposition. However, organisms without the conserved RNAi pathways, like Saccharomyces cerevisiae, must use other mechanisms to prevent transposon movement. Here, we provide evidence that antisense (AS) RNAs from the retrovirus-like element Ty1 inhibit retrotransposition posttranslationally in Saccharomyces. Multiple Ty1AS transcripts overlap Ty1 sequences necessary for copy number control (CNC) and inhibit transposition in trans. Altering Ty1 copy number or deleting sequences in the CNC region that are required for reverse transcription affect Ty1AS RNA level and Ty1 movement. Ty1AS RNAs are enriched in viruslike particles, and are associated with a dramatic decrease in the level of integrase, less reverse transcriptase, and an inability to synthesize Ty1 cDNA. Thus, Ty1AS RNAs are part of an intrinsic mechanism that limits retrotransposition by reducing the level of proteins required for replication and integration.retrotransposon ͉ virus-like particles ͉ RNA interference ͉ Saccharomyces R etrotransposons replicate through an RNA intermediate and can comprise over half the genome in many eukaryotes. To maintain genome stability, forms of RNAi have evolved to inhibit transposition (1). However, Saccharomyces cerevisiae lacks the genes required for RNAi, yet still maintains control over Ty1 retrotransposition. Ty1 elements and retroviruses have similar structures and strategies for gene expression, and encode functionally equivalent Gag and Pol proteins protease (PR), integrase (IN), and reverse transcriptase (RT) (2). Ty1 mRNA has unique subterminal 5Ј (U5) and 3Ј (U3) sequence motifs and a terminally repetitious (R) region. These sequences are required for reverse transcription and integration and form the U3-R-U5 segments of the LTR that bracket the element in the genome. Adjacent to U5 is the primer-binding site (pbs), where tRNA-Met i anneals with Ty1 mRNA to initiate reverse transcription within cytoplasmic virus-like particles (VLPs). Although not completely defined, sequences within GAG also enhance Ty1 mRNA dimer formation and packaging into VLPs (3, 4). The primary translation products are Gag-p49 and Gag-Pol-p199 that are cleaved by PR to form mature Gag-p45, PR-p20, IN-p71, and RT-p63. An association between IN and RT is required for reverse transcription in vivo and RT activity in vitro (5-7). Retrotransposition is completed by IN-mediated integration of Ty1 cDNA into the genome.Despite high levels of Ty1 mRNA and many functional elements in the genome, transposition occurs at a low rate (8-10). Cells also contain a low level of mature Ty1 proteins (11), and few VLPs are present (12). When an active Ty1 element is fused to the GAL1 promoter and carried on a multicopy pGTy1 plasmid (13), galactose induction overcomes the barriers to transposition. However, the mechanism underlying this obse...

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Genomic demography: a life-history analysis of transposable element evolution

Cited by 32 publications

References 31 publications

Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside

Genome evolution mediated by Ty elements in <i>Saccharomyces</i>

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

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