Evolution of the Transposable Element Mariner in Drosophila Species

The distribution of the transposable element mariner was examined in the genus Drosophila. Among the eight species comprising the melanogaster species subgroup, the element is present in D. mauritiana, D. simulans, D. sechellia, D. yakuba and D. teissieri, but it is absent in D. melanogaster, D. erecta and D. orena. Multiple copies of mariner were sequenced from each species in which the element occurs. The inferred phylogeny of the elements and the pattern of divergence were examined in order to evaluate whether horizontal transfer among species or stochastic loss could better account for the discontinuous distribution of the element among the species. The data suggest that the element was present in the ancestral species before the melanogaster subgroup diverged and was lost in the lineage leading to D. melanogaster and the lineage leading to D. erecta and D. orena. This inference is consistent with the finding that mariner also occurs in members of several other species subgroups within the overall melanogaster species group. Within the melanogaster species subgroup, the average divergence of mariner copies between species was lower than the coding region of the alcohol dehydrogenase (Adh) gene. However, the divergence of mariner elements within species was as great as that observed for Adh. We conclude that the relative sequence homogeneity of mariner elements within species is more likely a result of rapid amplification of a few ancestral elements than of concerted evolution. The mariner element may also have had unequal mutation rates in different lineages.     

Evidence for recent horizontal transfer of gypsy-homologous LTR-retrotransposon gtwin into Drosophila erecta followed by its amplification with multiple aberrations

Long terminal repeat (LTR) retrotransposon gtwin was initially discovered in silico, and then it was isolated as gypsy-homologous sequence from Drosophila melanogaster strain, G32. The presence of ORF3 suggests, that gtwin, like gypsy, may be an endogenous retrovirus, which can leave the cell and infect another one. Therefore, in this study we decided to investigate the distribution of gtwin in different species of the melanogaster subgroup in order to find out whether gtwin can be transferred horizontally as well as vertically. Gtwin was found in all 9 species of this subgroup, hence it seems to have inhabited the host genomes for a long time. In addition, we have shown that in the Drosophila erecta genome two gtwin families are present. The first one has 93% of identity to D. melanogaster element and is likely to be a descendant of gtwin that existed in Drosophila before the divergence of the melanogaster subgroup species. The other one has >99% of identity to D. melanogaster gtwin. The most reasonable explanation is that this element has been recently horizontally transferred between D. melanogaster and D. erecta. The number and variety of gtwin copies from the "infectious" family suggest that after the horizontal transfer into D. erecta genome, gtwin underwent amplification and aberrations, leading to the rise of its diverse variants.     

Closely related species of Drosophila can contain different libraries of middle repetitive DNA sequences

Very few of the middle repetitive DNA sequences found in Drosophila melanogaster are present in all of the species of the D. melanogaster subgroup. One member of the subgroup, D. erecta, lacks most of the families of repetitive elements from D. melanogaster (including copia and 412) but possesses many other families not present in the D. melanogaster genome. Other species in the subgroup possess some families in these two species and lack others. From this we conclude that most individual middle repetitive families are highly unstable components of the Drosophila genome over short periods of evolutionary time.     

Widespread occurence of mariner transposons in coastal crabs

Mariner-like elements (MLEs) are ubiquitous DNA mobile elements found in almost all eukaryote genomes. Nevertheless most of the known copies are inactive and the question of the genome invasion by MLEs remains largely hypothetical. We have previously reported the presence of highly homologous copies of MLEs in the genome of phylogenetically distant crustacea living in the same hydrothermal environment suggesting the possibility of horizontal transfer. In order to further support the hypothesis that horizontal transmission of MLEs might occur between crustacean sympatric species, we described here 85 MLE sequences found in the genome of a large spectrum of coastal crab species. The number of the MLEs copies in genomes was variable. Half of these MLEs fit with the irritans subfamily of MLEs whereas the second half grouped in a new subfamily called marmoratus. In addition, a molecular phylogeny of crabs was established by using the 16S information. The comparison between 16S and MLEs based trees reveals their incongruence, and suggests either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral MLE polymorphism followed by different evolution and stochastic loss.     

Vertical Transmission of the Retrotransposable Elements R1 and R2 during the Evolution of the Drosophila Melanogaster Species Subgroup

R1 and R2 are non-long-terminal repeat retrotransposable elements that insert into specific sequences of insect 28S ribosomal RNA genes. These elements have been extensively described in Drosophila melanogaster. To determine whether these elements have been horizontally or vertically transmitted, we characterized R1 and R2 elements from the seven other members of the melanogaster species subgroup by genomic blotting and nucleotide sequencing. Each species was found to have homogeneous families of R1 and R2 elements with the exception of erecta and orena, which have no R2 elements. The DNA sequences of multiple R1 and R2 copies from each species indicated nucleotide divergence within each species averaged only 0.48% for R1 and 0.35% for R2, well below the level of divergence among the species. Most copies of R1 and R2 (40 of 47) sequenced from the seven species were potentially functional, as indicated by the absence of premature termination codons or translational frameshifts that would destroy the open reading frame of the element. The sequence relationships of both the R1 and R2 elements from the various members of the melanogaster subgroup closely followed that of the species phylogeny, suggesting that R1 and R2 have been stably maintained by vertical transmission since the origin of this species subgroup 17-20 million years ago. The remarkable stability of R1 and R2, compared to what has been suggested for transposable elements that insert at multiple locations in these same species, may be due to their unique specificity for sites in the rRNA gene locus. Under low copy number conditions, when it is essential for any mobile element to transpose, the insertion specificities of R1 and R2 ensure uniform developmentally regulated target sites that can be occupied with little or no detrimental effect on the host.     

Intra- and interspecies variation among Bari-1 elements of the melanogaster species group.

We have investigated the distribution of sequences homologous to Bari-1, a Tc1-like transposable element first identified in Drosophila melanogaster, in 87 species of the Drosophila genus. We have also isolated and sequenced Bari-1 homologues from D. simulans, D. mauritiana, and D. sechellia, the species constituting with D. melanogaster the melanogaster complex, and from D. diplacantha and D. erecta, two phylogenetically more distant species of the melanogaster group. Within the melanogaster complex the Bari-1 elements are extremely similar to each other, showing nucleotide identity values of at least 99.3%. In contrast, Bari-1-like elements from D. diplacantha and D. erecta are on average only 70% similar to D. melanogaster Bari-1 and are usually defective due to nucleotide deletions and/or insertions in the ORFs encoding their transposases. In D. erecta the defective copies are all located in the chromocenter and on chromosome 4. Surprisingly, while D. melanogaster Bari-1 elements possess 26-bp inverted terminal repeats, their D. diplacantha and D. erecta homologues possess long inverted terminal repeats similar to the terminal structures observed in the S elements of D. melanogaster and in several other Tc1-like elements of different organisms. This finding, together with the nucleotide and amino acid identity level between D. diplacantha and D. erecta elements and Bari-1 of D. melanogaster, suggests a common evolutionary origin and a rapid diversification of the termini of these Drosophila Tc1-like elements.     

Identical satellite DNA sequences in sibling species of Drosophila

The evolution of simple satellite DNAs was examined by DNA-DNA hybridization of ten Drosophila melanogaster satellite sequences to DNAs of the sibling species, Drosophila simulans and Drosophila erecta. Seven of these repeat types are present in tandem arrays in D. simulans and each of the ten sequences is repeated in D. erecta. In thermal melts, six of the seven satellite sequences in D. simulans and seven of the ten sequences in D. erecta melted within 1 deg.C of the corresponding values in D. melanogaster. The remaining sequences melted within 3 deg.C of the homologous hybrids. Therefore, there is little or no alteration in those satellite sequences held in common, despite a period of about ten million years since the divergence of D. melanogaster and D. simulans from a common ancestor. Simple satellite sequences appear to be more highly conserved than coding regions of the genome, on a per nucleotide basis. Since multiple copies of three satellite sequences could not be detected in D. simulans yet are present in D. erecta, a species more distantly related to D. melanogaster than is D. simulans, these sequences show discontinuities in evolution. There were major quantitative variations between species, showing that satellite DNAs are prone to massive amplification or diminution events over timespans as short as those separating sibling species. In D. melanogaster, these sequences amount to 21% of the genome but only 5% in D. simulans and 0.4% in D. erecta. There was a general trend of lower abundance with evolutionary distance for most satellites, suggesting that the amounts of different satellite sequences do not vary independently during evolution.     

A highly repetitive, mariner-like element in the genome of Hyalophora cecropia.

A highly repetitive DNA element, homologous to the mariner transposon of Drosophila mauritiana was found in the intron of the gene for cecropin A, an antibacterial peptide from the Cecropia moth. The mariner-like elements (MLE) represent a homogeneous population with a copy number of about 1000/genome. Sequencing analysis showed it to be 1255 base pairs long, including 38-base pair terminal inverted repeats. The MLE contains a defective reading frame. Nevertheless, the putative product is clearly homologous to the predicted translation product encoded by mariner. In consonance is also the fact that the inverted repeats are highly conserved between the two elements and that the overall DNA homology is 48%. Since the mariner element is present in several Drosophila species closely related to Drosophila melanogaster and since MLE is present in the lepidopteran Cecropia, a route of horizontal transfer is indicated rather than vertical transmission from a common ancestor. This suggests the possible use of mariner for the construction of an interspecies vector.     

Isolation and characterization of seventy-nine full-length <Emphasis Type="Italic">mariner</Emphasis>-like transposase genes in the Bambusoideae subfamily

Mariner-like elements (MLEs) are the most diverse and widespread transposable elements, with members of the MLE superfamily found in fungi, plants, ciliates and animals. In a previous study, we characterized 82 MLE transposase gene fragments (average length 383 bp) in 44 bamboo species, indicating that MLEs are widespread, abundant and diverse in the Bambusoideae subfamily. In this study, we isolated 79 full-length MLE transposase genes from 63 bamboo species representing 38 genera in six subtribes mainly found in China. The transposases were highly conserved, mostly uniform in length and contained intact DNA-binding motifs and DD39D catalytic domains with few notable frameshift, indel and nonsense mutations. This suggested the MLEs are probably still mobile, not yet affected by vertical inactivation. A phylogenetic tree of the Bambusoideae subfamily established using ribosomal DNA internal transcribed spacer sequences was incongruent with a second tree based on the MLE transposase genes. This evidence, together with the presence of near-identical MLEs in distantly related species and diverse MLEs in closely related species, indicates that MLEs have evolved in a distinct manner, probably independently of speciation events in the subfamily. The evolution and diversity of MLE transposase genes in the Bambusoideae subfamily is discussed.     

Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes

I present here evidence of remarkable local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. The substitution pattern at 10 loci in the telomeric region of the X chromosome was studied for four species of the Drosophila melanogaster species subgroup. Drosophila orena and Drosophila erecta are clearly the most closely related species pair (the erecta complex) among the four species studied; however, the overall data at the 10 loci revealed a clear dichotomy in the silent substitution patterns between the AT-biased- substitution melanogaster and erecta lineages and the GC-biased-substitution yakuba and orena lineages, suggesting two or more independent changes in GC/AT substitution biases. More importantly, the results indicated a between- loci heterogeneity in GC/AT substitution bias in this small region independently in the yakuba and orena lineages. Indeed, silent substitutions in the orena lineage were significantly biased toward G and C at the consecutive yellow, lethal of scute, and asense loci, but they were significantly biased toward A and T at sta. The substitution bias toward G and C was centered in different areas in yakuba (significantly biased at EG:165H7.3, EG:171D11.2, and suppressor of sable). The similar silent substitution patterns in coding and noncoding regions, furthermore, suggested mutational biases as a cause of the substitution biases. On the other hand, previous study reveals that Drosophila yakuba has about 20-fold higher crossover frequencies in the telomeric region of the X chromosome than does D. melanogaster; this study revealed that the total genetic map length of the yakuba X chromosome was only about 1.5 times as large as that of melanogaster and that the map length of the X-telomeric y-sta region did not differ between Drosophila yakuba and D. erecta. Taken together, the data strongly suggested that an approximately 20- fold reduction in the X-telomeric crossover frequencies occurred in the ancestral population of D. melanogaster after the melanogaster-yakuba divergence but before the melanogaster-simulans divergence.     

Reproductive Isolation and Morphogenetic Evolution in Drosophila Analyzed by Breakage of Ethological Barriers

This article reports the breaking of ethological barriers through the constitution of soma-germ line chimeras between species of the melanogaster subgroup of Drosophila, which are ethologically isolated. Female Drosophila yakuba and D. teissieri germ cells in a D. melanogaster ovary produced functional oocytes that, when fertilized by D. melanogaster sperm, gave rise to sterile yakuba-melanogaster and teissieri-melanogaster male and female hybrids. However, the erecta-melanogaster and orena-melanogaster hybrids were lethal, since female D. erecta and D. orena germ cells in a D. melanogaster ovary failed to form oocytes with the capacity to develop normally. This failure appears to be caused by an altered interaction between the melanogaster soma and the erecta and orena germ lines. Germ cells of D. teissieri and D. orena in a D. melanogaster testis produced motile sperm that was not stored in D. melanogaster females. This might be due to incompatibility between the teissieri and orena sperm and the melanogaster seminal fluid. A morphological analysis of the terminalia of yakuba-melanogaster and teissieri-melanogaster hybrids was performed. The effect on the terminalia of teissieri-melanogaster hybrids of a mutation in doublesex, a regulatory gene that controls the development of the terminalia, was also investigated.     

Distribution of the bilbo non-LTR retrotransposon in Drosophilidae and its evolution in the Drosophila obscura species group

The bilbo element is a non-LTR retrotransposon isolated from Drosophila subobscura. We conducted a distribution survey by Southern blot for 52 species of the family Drosophilidae, mainly from the obscura and melanogaster groups. Most of the analyzed species bear sequences homologous to bilbo from D. subobscura. In the obscura group, species from the same species subgroup also share similar Southern blot patterns. To investigate the phylogenetic relationship among these elements, we analyzed eight copies of a short sequence of the element from several species of the obscura group. The obtained phylogram agrees with the phylogeny of the species, which suggests vertical transmission of the element.     

The <Emphasis Type="Italic"> GATE </Emphasis>retrotransposon in<Emphasis Type="Italic"> Drosophila melanogaster</Emphasis>: mobility in heterochromatin and aspects of its expression in germline tissues

A full-length copy of the retrotransposon GATE was identified as an insertion in the tandemly repeated, heterochromatic, Stellate genes, which are expressed in the testis of Drosophila melanogaster. Sequencing of this heterochromatic GATE copy revealed that it is closely related to the BEL retrotransposon, a representative of the recently defined BEL-like group of LTR retrotransposons. This copy contains identical LTRs, indicating that the insertion is a recent event. By contrast, the euchromatic part of the D. melanogaster genome contains only profoundly damaged GATE copies or fragments of the transposon. The preferential localization of GATE sequences in heterochromatin was confirmed for the other species in the melanogaster subgroup. The level of GATE expression is dramatically increased in ovaries, but not in testes, of spn-E(1) homozygous flies. We speculate that spn-E is involved in the silencing of GATE via an RNA interference mechanism.     

Changes in the recombinational environment affect divergence in the yellow gene of Drosophila

The complete coding region of the yellow (y) gene was sequenced in different Drosophila species. In the species of the melanogaster subgroup (D. melanogaster, D. simulans, D. mauritiana, D. yakuba, and D. erecta), this gene is located at the tip of the X chromosome in a region with a strong reduction in recombination rate. In contrast, in D. ananassae (included in the ananassae subgroup of the melanogaster group) and in the obscura group species (D. subobscura, D. madeirensis, D. guanche, and D. pseudoobscura), the y gene is located in regions with normal recombination rates. As predicted by the hitchhiking and background selection models, this change in the recombinational environment affected synonymous divergence in the y-gene-coding region. Estimates of the number of synonymous substitutions per site were much lower between the obscura group species and D. ananassae than between the species of the obscura group and the melanogaster subgroup. In fact, a highly significant increase in the rate of synonymous substitution was detected in all lineages leading to the species of the melanogaster subgroup relative to the D. ananassae lineage. This increase can be explained by a higher fixation rate of mutations from preferred to unpreferred codons (slightly deleterious mutations). The lower codon bias detected in all species of the melanogaster subgroup relative to D. ananassae (or to the obscura group species) would be consistent with this proposal. Therefore, at least in Drosophila, changes in the recombination rate in different lineages might cause deviations of the molecular-clock hypothesis and contribute to the overdispersion of the rate of synonymous substitution. In contrast, the change in the recombinational environment of the y gene has no detectable effect on the rate of amino acid replacement in the Yellow protein.     

Evolution of gypsy endogenous retrovirus in the Drosophila obscura species group

The Ty3/gypsy family of retroelements is closely related to retroviruses, and some of their members have an open reading frame resembling the retroviral gene env. Sequences homologous to the gypsy element from Drosophila melanogaster are widely distributed among Drosophila species. In this work, we report a phylogenetic study based mainly on the analysis of the 5' region of the env gene from several species of the obscura group, and also from sequences already reported of D. melanogaster, Drosophila virilis, and Drosophila hydei. Our results indicate that the gypsy elements from species of the obscura group constitute a monophyletic group which has strongly diverged from the prototypic D. melanogaster gypsy element. Phylogenetic relationships between gypsy sequences from the obscura group are consistent with those of their hosts, indicating vertical transmission. However, D. hydei and D. virilis gypsy sequences are closely related to those of the affinis subgroup, which could be indicative of horizontal transmission.     

Distribution of the retrotransposable element 412 in Drosophila species

Copy numbers of sequences homologous to the Drosophila melanogaster retrotransposable element 412, their distribution between the chromosome arms and the chromocenter, and whether they contain full- size copies were analyzed for 55 species of the Drosophila genus. Element 412 insertion sites were detected on the chromosome arms of D. melanogaster, Drosophila simulans, and a few species of the obscura group, but the chromocenter was labeled in almost all species. The presence of element 412 sequences in the majority of species shows that this element has a long evolutionary history in Drosophilidae, although it may have recently invaded the chromosomes in some species, such as D. simulans. Differences in copy number between species may be due to population size or specific endogenous or environmental factors and may follow the worldwide invasion of the species. Putative full-length copies were detected in the chromocenters of some species with no copies on the chromosome arms, suggesting that the chromocenter may be a shelter for such copies and not only for deleted ones.