Multiple LTR-retrotransposon families in the asexual yeast Candida albicans

We have begun a characterization of the long terminal repeat (LTR) retrotransposons in the asexual yeast Candida albicans. A database of assembled C. albicans genomic sequence at Stanford University, which represents 14.9 Mb of the 16-Mb haploid genome, was screened and >350 distinct retrotransposon insertions were identified. The majority of these insertions represent previously unrecognized retrotransposons. The various elements were classified into 34 distinct families, each family being similar, in terms of the range of sequences that it represents, to a typical Ty element family of the related yeast Saccharomyces cerevisiae. These C. albicans retrotransposon families are generally of low copy number and vary widely in coding capacity. For only three families, was a full-length and apparently intact retrotransposon identified. For many families, only solo LTRs and LTR fragments remain. Several families of highly degenerate elements appear to be still capable of transposition, presumably via trans-activation. The overall structure of the retrotransposon population in C. albicans differs considerably from that of S. cerevisiae. In that species, retrotransposon insertions can be assigned to just five families. Most of these families still retain functional examples, and they generally appear at higher copy numbers than the C. albicans families. The possibility that these differences between the two species are attributable to the nonstandard genetic code of C. albicans or the asexual nature of its genome is discussed. A region rich in retrotransposon fragments, that lies adjacent to many of the CARE-2/Rel-2 sub-telomeric repeats, and which appears to have arisen through multiple rounds of duplication and recombination, is also described.     

Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe

The complete DNA sequence of the genome of Schizosaccharomyces pombe provides the opportunity to investigate the entire complement of transposable elements (TEs), their association with specific sequences, their chromosomal distribution, and their evolution. Using homology-based sequence identification, we found that the sequenced strain of S. pombe contained only one family of full-length transposons. This family, Tf2, consisted of 13 full-length copies of a long terminal repeat (LTR) retrotransposon. We found that LTR-LTR recombination of previously existing transposons had resulted in extensive populations of solo LTRs. These included 35 solo LTRs of Tf2, as well as 139 solo LTRs from other Tf families. Phylogenetic analysis of solo Tf LTRs reveals that Tf1 and Tf2 were the most recently active elements within the genome. The solo LTRs also served as footprints for previous insertion events by the Tf retrotransposons. Analysis of 186 genomic insertion events revealed a close association with RNA polymerase II promoters. These insertions clustered in the promoter-proximal regions of genes, upstream of protein coding regions by 100 to 400 nucleotides. The association of Tf insertions with pol II promoters was very similar to the preference previously observed for Tf1 integration. We found that the recently active Tf elements were absent from centromeres and pericentromeric regions of the genome containing tandem tRNA gene clusters. In addition, our analysis revealed that chromosome III has twice the density of insertion events compared to the other two chromosomes. Finally we describe a novel repetitive sequence, wtf, which was also preferentially located on chromosome III, and was often located near solo LTRs of Tf elements.     

The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

Long terminal repeat (LTR) retrotransposons are major components of plant genomes influencing genome size and evolution. Using two separate approaches, we identified the Ty1-copia retrotransposon families Cotzilla and SALIRE in the Beta vulgaris (sugar beet) genome. While SALIRE elements are similar to typical Ty1-copia retrotransposons, Cotzilla elements belong to a lineage called Sireviruses. Hallmarks of Cotzilla retrotransposons are the existence of an additional putative env-like open reading frame upstream of the 3′LTR, an extended gag region, and a frameshift separating the gag and pol genes. Detected in a c ₀ t-1 DNA library, Cotzilla elements belong to the most abundant retrotransposon families in B. vulgaris and are relatively homogenous and evolutionarily young. In contrast, the SALIRE family has relatively few copies, is diverged, and most likely ancient. As revealed by fluorescent in situ hybridization, SALIRE elements target predominantly gene-rich euchromatic regions, while Cotzilla retrotransposons are abundant in the intercalary and pericentromeric heterochromatin. The analysis of two retrotransposons from the same subclass contrasting in abundance, age, sequence diversity, and localization gives insight in the heterogeneity of LTR retrotransposons populating a plant genome.     

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

We initially analyzed 11 families of low- and middle-copy-number long terminal repeat (LTR) retrotransposons in rice to determine how their structures have diverged from their predicted ancestral forms. These elements, many highly fragmented, were identified on the basis of sequence homology and structural characteristics. The 11 families, totaling 1000 elements, have copy numbers ranging from 1 to 278. Less than one-quarter of these elements are intact, whereas the remaining are solo LTRs and variously truncated fragments. We also analyzed two highly repetitive families (Osr8 and Osr30) of LTR retrotransposons and observed the same results. Our data indicate that unequal homologous recombination and illegitimate recombination are primarily responsible for LTR-retrotransposon removal. Further analysis suggests that most of the detectable LTR retrotransposons in rice inserted less than 8 million years ago, and have now lost over two-thirds of their encoded sequences. Hence, we predict that the half-life of LTR-retrotransposon sequences in rice is less than 6 million years. Moreover, our data demonstrate that at least 22% (97 Mb) of the current rice genome is comprised of LTR-retrotransposon sequences, and that more than 190 Mb of LTR-retrotransposon sequences have been deleted from the rice genome in the last 8 million years.     

A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion

Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposons and genome expansion in a large genome, we have studied a 66-kb contiguous sequence at the Rar1 locus of barley in detail. Three genes were identified in the 66-kb contig, clustered within an interval of 18 kb. Inspection of sequences flanking the gene space unveiled four novel retroelements, designated Nikita, Sukkula, Sabrina, and BAGY-2 and several units of the known BARE-1 element. The retroelements identified are responsible for at least 15 integration events, predominantly arranged as multiple nested insertions. Strikingly, most of the retroelements exist as solo LTRs (Long Terminal Repeats), indicating that unequal crossing over and/or intrachromosomal recombination between LTRs is a common feature in barley. Our data suggest that intraelement recombination events deleted most of the original retrotransposon sequences, thereby providing a possible mechanism to counteract retroelement-driven genome expansion.     

Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes

LTR-containing retrotransposons reverse transcribe their RNA genomes, and the resulting cDNAs are integrated into the genome by the element-encoded integrase protein. The yeast LTR retrotransposon Ty1 preferentially integrates into a target window upstream of tDNAs (tRNA genes) in the yeast genome. We investigated the nature of these insertions and the target window on a genomic scale by analyzing several hundred de novo insertions upstream of tDNAs in two different multicopy gene families. The pattern of insertion upstream of tDNAs was nonrandom and periodic, with peaks separated by ~80 bp. Insertions were not distributed equally throughout the genome, as certain tDNAs within a given family received higher frequencies of upstream Ty1 insertions than others. We showed that the presence and relative position of additional tDNAs and LTRs surrounding the target tDNA dramatically influenced the frequency of insertion events upstream of that target.     

Daidara: A gigantic Gypsy LTR retrotransposon lineage in the springtail Allacma fusca genome

Long terminal repeat (LTR) retrotransposons are the major contributor to genome size expansion, as in the cases of the maize genome or the axolotl genome. Despite their impact on the genome size, the length of each retrotransposon is limited, compared to DNA transposons, which sometimes exceed over 100 kb. The longest LTR retrotransposon known to date is Burro-1 from the planarian Schmidtea medierranea, which is around 35.7 kb long. Here through bioinformatics analysis, a new lineage of gigantic LTR retrotransposons, designated Daidara, is reported from the springtail Allacma fusca genome. Their entire length (25–33 kb) rivals Burro families, while their LTRs are shorter than 1.5 kb, in contrast to other gigantic LTR retrotransposon lineages Burro and Ogre, whose LTRs are around 5 kb long. Daidara encodes three core proteins corresponding to gag, pol, and an additional protein of unknown function. The phylogenetic analysis supports the independent gigantification of Daidara from Burro or Ogre.     

Chromodomains direct integration of retrotransposons to heterochromatin

The enrichment of mobile genetic elements in heterochromatin may be due, in part, to targeted integration. The chromoviruses are Ty3/gypsy retrotransposons with chromodomains at their integrase C termini. Chromodomains are logical determinants for targeting to heterochromatin, because the chromodomain of heterochromatin protein 1 (HP1) typically recognizes histone H3 K9 methylation, an epigenetic mark characteristic of heterochromatin. We describe three groups of chromoviruses based on amino acid sequence relationships of their integrase C termini. Genome sequence analysis indicates that representative chromoviruses from each group are enriched in gene-poor regions of the genome relative to other retrotransposons, and when fused to fluorescent marker proteins, the chromodomains target proteins to specific subnuclear foci coincident with heterochromatin. The chromodomain of the fungal element, MAGGY, interacts with histone H3 dimethyl- and trimethyl-K9, and when the MAGGY chromodomain is fused to integrase of the Schizosaccharomyces pombe Tf1 retrotransposon, new Tf1 insertions are directed to sites of H3 K9 methylation. Repetitive sequences such as transposable elements trigger the RNAi pathway resulting in their epigenetic modification. Our results suggest a dynamic interplay between retrotransposons and heterochromatin, wherein mobile elements recognize heterochromatin at the time of integration and then perpetuate the heterochromatic mark by triggering epigenetic modification.     

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

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 > or =99% 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.     

Sexual behavior and its pheromonal regulation in ascosporogenous yeasts

We reviewed our investigations on sexual behaviors and interactions including sexual cell agglutination and pheromone action mainly in non-conventional yeasts, Hansenula anomala, H. wingei, Pichia amethionina, P. heedi, P. opuntiae, Saccharomyces kluyveri, S. globsus, S. exiguus, Saccharomycodes ludwigii. The techniques and genetic models including the cassette model and alpha 1-alpha 2 hypothesis which had been developed largely in S. cerevisiae were applicable to these yeasts in principle. The sexual agglutination was distinctly species-specific while sex pheromones were cross-reactive beyond species' barriers. The successful induction of heterothallic strains from homothallic strains in S. exiguus by mutagenesis enabled to the subsequent biochemical and genetical analysis of sexual behavior in the yeast. The phylogenetic consideration on sex differentiation is also included.     

Nht2, a copia LTR retrotransposon from a conditionally dispensable chromosome in Nectria haematococca

In the plant pathogenic ascomycete Nectria haematococca mating population (MP) VI, the conditionally dispensable chromosomes are unstable during sexual reproduction. During mapping of such a chromosome, three dispersed repeats were identified. Nht2, one of these repeated elements, is a long terminal repeat (LTR) retrotransposon that is 5.9 kb in length. Its deduced amino acid sequence is homologous to the four enzymatic domains characteristic of copia retrotransposons, but it contains multiple stop codons and probably is no longer able to transpose autonomously. Nht2's LTRs differ at ten positions and the characteristics of these differences resemble the changes induced by repeat-induced point mutation (RIP) in Neurospora crassa. The likelihood that Nectria haematococca MP VI has a RIP-like process, however, is reduced by the fact that a multi-copy transposon cloned from the same ascospore isolate as Nht2 encodes an intact open reading frame. Nht2 is broadly distributed among isolates collected from a variety of host plants. A limited survey of three field isolates suggests that Nht2 is on only one or a few chromosomes in every genome. Nht2's degeneracy and its widespread distribution within the species both suggest that it is an ancient element within N. haematococca MP VI.