Insertion sites of the transposable elementmariner are fixed in the genome ofDrosophila sechellia

Summary The abundance of the transposable elementmariner differs dramatically in the genomes of the closely related speciesDrosophila simulans, D. mauritiana, D. sechellia, andD. melanogaster. Natural populations ofD. simulans andD. mauritiana have 1–10 and 20–30 copies per diploid genome, respectively, and the insertion sites are polymorphic. The element has not been found inD. melanogaster. In this paper we show thatD. sechellia, a species endemic to the Seychelles Islands, contains only twomariner elements that are at fixed sites in the genome. One element, inserted in chromosome 2R at 51A1–2, contains three deletions and is missing much of the 3 end. The other element, inserted in chromosome 3L at 64A10–11, is the full length of 1286 bp. Although the sequence of the full-length element is polymorphic in populations ofD. sechellia, at least some of the sequences are closely related to elements fromD. simulans andD. mauritiana that are known to be active. However, judging from the progeny of crosses betweenD. sechellia andD. simulans, the biological activity of the full-lengthD. sechellia element appears to be low, either because of the nucleotide sequence of the element or because of its position in the genome, or both.     

Themariner transposable element in natural populations ofDrosophila teissieri

Themariner transposable elements of several natural populations ofDrosophila teissieri, a rainforest species endemic to tropical Africa, were studied. Natural populations trapped along a transect from Zimbabwe to the Ivory Coast were analyzed by Southern blotting, in situ hybridization, cloning, and sequencing of PCR products. The Brazzaville population had some full-length elements, while the remaining populations had mainly deleted elements. The main class of deleted elements lacked a 500-bp segment. A mechanism is proposed that could generate such elements rapidly. In situ hybridizations showed that there are nomariner elements in pericentromeric heterochromatin. Finally, the phylogeny of theMos1-likemariner full-length elements is consistent with vertical transmission from the ancestor of themelanogaster subgroup. Correspondence to: P. Capy     

Molecular Phylogeny of the <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> Species Subgroup

Although molecular and phenotypic evolution have been studied extensively in Drosophila melanogaster and its close relatives, phylogenetic relationships within the D. melanogaster species subgroup remain unresolved. In particular, recent molecular studies have not converged on the branching orders of the D. yakuba–D. teissieri and D. erecta–D. orena species pairs relative to the D. melanogaster–D. simulans–D. mauritiana–D. sechellia species complex. Here, we reconstruct the phylogeny of the melanogaster species subgroup using DNA sequence data from four nuclear genes. We have employed vectorette PCR to obtain sequence data for orthologous regions of the Alcohol dehydrogenase (Adh), Alcohol dehydrogenase related (Adhr), Glucose dehydrogenase (Gld), and rosy (ry) genes (totaling 7164 bp) from six melanogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba, D. erecta, and D. orena) and three species from subgroups outside the melanogaster species subgroup [D. eugracilis (eugracilis subgroup), D. mimetica (suzukii subgroup), and D. lutescens (takahashii subgroup)]. Relationships within the D. simulans complex are not addressed. Phylogenetic analyses employing maximum parsimony, neighbor-joining, and maximum likelihood methods strongly support a D. yakuba–D. teissieri and D. erecta–D. orena clade within the melanogaster species subgroup. D. eugracilis is grouped closer to the melanogaster subgroup than a D. mimetica–D. lutescens clade. This tree topology is supported by reconstructions employing simple (single parameter) and more complex (nonreversible) substitution models. Present address (Ryan M. David): University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78284, USA     

Evolution of thedec-1 eggshell locus inDrosophila. I. Restriction site mapping and limited sequence comparison in themelanogaster species subgroup

Summary We have analyzed 18 kb of DNA in and upstream of thedefective chorion-1 (dec-1) locus of the eight known species of themelanogaster species subgroup ofDrosophila. The restriction maps ofD. simulans, D. mauritiana, D. sechellia, D. erecta, andD. orena are shown to have basically the restriction map ofD. melanogaster, whereas the maps ofD. teissieri andD. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65–200 bp) is found in a repeated sequence of the central transcribed region ofD. melanogaster, D. simulans, andD. erecta. Restriction site mapping indicated that thedec-1 gene is highly conserved in themelanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5 translated region. The 5 flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within themelanogaster species subgroup except that theerecta-orena pair is placed closer to themelanogaster complex than toD. teissieri andD. yakuba.     

Mobilization of a Hobo-related Sequence in the Genome of Drosophila simulans

The hobo transposable element can occur under three forms in the Drosophila genome: as a complete element (also called canonical), as internally deleted copies, or as hobo-related sequences (relics). Some evidence indicated that canonical elements and internally deleted copies are recent acquisitions of Drosophila genomes, while the “relics” are old components, normally degenerated and immobile. Here we present the characterization of a hobo-related sequence, found in the genome of a hypermutable strain of D. simulans, which insertion into the white locus raised a de novo white mutation. It is a shorter hobo related element presenting, overall, roughly 18% of divergence at the DNA level from the canonical hobo, with many indels that make clear this element is defective. However, its ITRs and flanking regions are extremely conserved. This is the first hobo “relic” showed to be mobilizable. We suggest, and point up some evidences, toward the idea that this sequence could have been mobilized by the canonical element. The presence of a similar “relic” element in D. sechellia allows us to suggest that these elements have been maintained mobilizable since the time of divergence between these species.     

Regulatory potential of nonautonomous mariner elements and subfamily crosstalk

Two naturally occurring nonautonomous mariner elements were tested in vivo for their ability to down-regulate excision of a target element in the presence of functional mariner transposase. The tested elements were the peach element isolated from Drosophila mauritiana which encodes a transposase that differs from the autonomous element Mos1 in four amino acid replacements, and the DTBZ1 element isolated from D. teissieri which encodes a truncated protein consisting of the first 132 residues at the amino end of the normally 345-residue transposase. We provide evidence that the protein from the peach element does interact to down-regulate wildtype transposase, indicating that at least some nonautonomous elements in natural populations that retain their open reading frame may play a regulatory role. In contrast, our tests reveal at most a weak interaction between transposase from the autonomous Mos1 element and the truncated protein from DTBZ1 and none between Mos1 transposase and that from the distantly related mariner-like element Himar1 identified in the horn fly Haematobia irritans. Hence, the extent of regulatory crosstalk between mariner-like elements may be limited to closely related ones. The evolutionary implications of these results are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization ofGandalf, a new inverted-repeat transposable element ofDrosophila koepferae

The cloning and characterization ofGandalf, a new DNA-transposing mobile element obtained from theDrosophila koepferae (repleta group) genome is described. A fragment ofGandalf was found in a middle repetitive clone that shows variable chromosomal localization. Restriction, Southern blot, PCR and sequencing analyses have shown that mostGandalf copies are about 1 kb long, are flanked by 12 by inverted terminal repeats and contain subterminal repetitive regions on both sides of the element. As with other elements of the DNA-transposing type (known as the Ac family), theGandalf element generates 8 by direct duplications at the insertion point. Coding region analysis has shown that the longer open reading frame found inGandalf copies could encode part of a protein. However, whether or not the 1 kb copies of the element are actually the active transposons remains to be elucidated.Gandalf shows a very low copy number inD. buzzatii, a sibling species ofD. koepferae. An attempt to induce interspecific hybrid dysgenesis in hybrids of these two species has been unsuccessful.     

Structural evolution of the Drosophila 5S ribosomal genes

We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5-flanking region (54–55 bp), the 3-flanking region (21–22 bp), and the internal spacer (149–206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6–17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps. Correspondence to: M. Wegnez     

The transposable element mariner can excise in non-drosophilid insects

Plasmid-based excision assays performed in embryos of two non-drosophilid species using the mariner transposable element from Drosophila mauritiana resulted in empty excision sites identical to those observed after the excision of mariner from D. mauritiana chromosomes. In the presence of the autonomous mariner element Mos1, excision products were recovered from D. melanogaster, D. mauritiana and the blowfly Lucilia cuprina. When a hsp82 heat shock promoter-Mos1 construct was used to supply mariner transposase, excision products were also recovered from the Queensland fruitfly Bactrocera tryoni. Analysis of DNA sequences at empty excision sites led us to hypothesise that the mariner excision/repair process involves the formation of a heteroduplex at the excision breakpoint. The success of these assays suggests that they will provide a valuable tool for assessing the ability of mariner and mariner-like elements to function in non-drosophilid insects and for investigating the basic mechanisms of mariner excision and repair.     

Survey of Mariner-Like Elements in the Housefly, Musca Domestica

The presence of mariner-like elements in four strains of the housefly, Musca domestica, was surveyed by PCR. Using the inverted terminal repeat (ITR) sequences of the Mos 1element as primers, DNAs were successfully amplified from all strains of the housefly. Southern blot analysis indicated that these amplified DNAs were repetitive sequences in the genome of M. domestica. Sequence analyses of cloned PCR products showed that they were 45% identical to the Mos 1element. These fragments appeared to be nonfunctional, because they contained no intact open reading frame (ORF) capable of encoding transposase. We conclude that these DNAs are degraded mariner-like elements (MLEs) in M. domestica. Because these endogenous MLEs in M. domesticado not encode any functional proteins, they probably would not affect the behavior of mariner-based vectors if such were introduced into this species as transformation vectors.     

Evolution of the threonine-glycine repeat region of the period gene in the melanogaster species subgroup of drosophila

Summary The Threonine-Glycine (Thr-Gly) region of the period gene (per) in Drosophila was compared in the eight species of the D. melanogaster subgroup. This region can be divided into a diverged variable-length segment which is flanked by more conserved sequences. The number of amino acids encoded in the variable-length region ranges from 40 in D. teissieri to 69 in D. mauritiana. This is similar to the range found within natural populations of D. melanogaster. It was possible to derive a Thr-Gly allele of one species from that of another by invoking hypothetical Thr-Gly intermediates. A phylogeny based on the more conserved flanking sequences was produced. The results highlighted some of the problems which are encountered when highly polymorphic genes are used to infer phylogenies of closely related species.     

Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920–1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster than to the chromocentral I elements in any species. No sequence difference was observed in the surveyed region between two chromosomal I elements isolated from D. melanogaster and one from D. simulans. These findings strongly support the idea that the defective chromocentral I elements of D. melanogaster originated before the species diverged and the chromosomal I elements were eliminated. The chromosomal I elements reinvaded natural populations of D. melanogaster recently, and were possibly introduced from D. simulans by horizontal transmission.     

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

Background

The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes.

Results

We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies.

Conclusions

This analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all “life cycle” stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-727) contains supplementary material, which is available to authorized users.     

Aurora, a non-mobile retrotransposon in Drosophila melanogaster heterochromatin

A novel retrotransposon, aurora, containing 324 by long terminal repeats (LTRs) was detected in Drosophila melanogaster as a 5 kb insertion in the heterochromatic Stellate gene. This insertion causes a 5 bp duplication of the integration site. Southern analysis and in situ hybridization data show that all detectable copies of aurora are immobilized in the D. melanogaster heterochromatin. However, mobile copies of aurora were revealed in the cuchromatin of D. simulans. The element was also found in various species of the melanogaster subgroup and in the D. virilis genome.The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession numbers X70361 and X70362     

Development time and pupation behavior in theDrosophila melanogaster subgroup (Diptera: Drosophilidae)

This study is an in-depth analysis of intersexual, intraspecific, and interspecific variability in larvopupal developmental time, pupation site preference, and larval and pupal survival of a number of isofemale lines of the speciesDrosophila mauritiana, D. melanogaster, D. sechellia, D. simulans, D. teissieri, andD. yakuba. There was no significant sex differences in pupation height, but females eclosed significantly earlier than males in all species. In addition, the suggestion of a strong negative correlation between larval developmental time and pupation height could not be confirmed in this study. The hypothesis that differences in pupation height provide a basis for niche partitioning between closely related species with overlapping distributions was tested by three planned orthogonal contrast analyses of variance. First, the two speciesD. teissieri andD. yakuba, with largely overlapping distribution, were significantly different in pupation height. Second, the two allopatric, nonoverlapping island speciesD. mauritiana andD. sechellia did not significantly differ in pupation height. However, the absence of a significant difference in the final contrast between the two cosmopolitan speciesD. melanogaster andD. simulans, which are often found together, makes us cautious to accept the hypothesis.     

The transposable element impala, a fungal member of the Tc1-mariner superfamily

A new transposable element has been isolated from an unstable niaD mutant of the fungus Fusarium oxysporum. This element, called impala, is 1280 nucleotides long and has inverted repeats of 27 bp. Impala inserts into a TA site and leaves behind a footprint when it excises. The inserted element, impala-160, is cis-active, but is probably trans-defective owing to several stop codons and frameshifts. Similarities exist between the inverted repeats of impala and those of transposons belonging to the widely dispersed mariner and Tc1 families. Moreover, translation of the open reading frame revealed three regions showing high similarities with Tc1 from Caenorhabditis elegans and with the mariner element of Drosophila mauritiana. The overall comparison shows that impala occupies an intermediate position between the mariner and Tcl-like elements, suggesting that all these elements belong to the same superfamily. The degree of relatedness observed between these elements, described in different kingdoms, raises the question of their origin and evolution.     

The LSP1-α gene is not dosage compensated in the Drosophila melanogaster species subgroup

The X-linked subunit of larval serum protein 1 (LSP1-) is shown to lack dosage compensation in six members of the melanogaster species subgroup, viz., Drosophila melanogaster, D. simulans, D. mauritiana, D. erecta, D. yakuba, and D. teissieri, by quantitative filter hybridization and by electrophoretic and autoradiographic analyses of fat body proteins. These results support the hypothesis that there is little selection pressure on the LSP1- gene to acquire dosage compensation.H.W.B. acknowledges a Commonwealth Scholarship. This work was supported by an SRC grant to D.B.R.     

The evolutionary genetics of thehobo transposable element in theDrosophila melanogaster complex

Hobo elements are a family of transposable elements found inDrosophila melanogaster and its three sibling species:D. simulans, D. mauritiana andD. sechellia. Studies inD. melanogaster have shown thathobo may be mobilized, and that the genetic effects of such mobilizations included the general features of hybrid dysgenesis: mutations, chromosomal rearrangements and gonadal dysgenis in F1 individuals. At the evolutionary level somehobo-hybridizing sequences have also been found in the other members of themelanogaster subgroup and in many members of the relatedmontium subgroup. Surveys of older collected strains ofD. melanogaster suggest that completehobo elements were absent prior to 50 years ago and that they have recently been introduced into this species by horizontal transfer. In this paper we review our findings and those of others, in order to precisely describe the geographical distribution and the evolutionary history ofhobo in theD. melanogaster complex. Studies of the DNA sequences reveal a different level of divergence between the groupD. melanogaster, D. simulans andD. mauritiana and the fourth speciesD. sechellia. The hypothesis of multiple transfers in the recent past into theD. melanogaster complex from a common outside source is discussed.     

Distribution of the Transposable Element Minos in the Genus Drosophila

We analyzed 28 species of the genus Drosophilafor the presence of the Tc1-like transposable element Minosusing Southern blot hybridization under high stringency conditions. The Minostransposon was found in members of both the Drosophilaand the Sophophorasubgenus showing a distribution that is wider if compared to other well-studied Drosophilatransposons such as the Pelement, hoboand mariner. The presence of Minos-hybridizing sequences was discontinuous in the Sophophorasubgenus, especially in the melanogasterspecies group. Using the Polymerase Chain Reaction we amplified a portion corresponding to the putative Minostransposase from different Drosophilaspecies. Cloning and sequence analysis of randomly selected Minoscopies from D. mojavensisis, D. saltansand D. willistonisupports the idea that event(s) of horizontal transfer may have contributed to the spreading of this transposon in the Drosophilagenus. This revised version was published online in July 2006 with corrections to the Cover Date.     

Horizontal transmission versus ancient origin:Mariner in the witness box

The transposable elementmariner has been found in many species ofDrosophilidae, several groups of Arthropods, and more recently in Platyhelminthes as well as in a phytopathogenic fungus. In the familyDrosophilidae, the distribution ofmariner among species shows many gaps, and its geographical distribution among endemic species is restricted to Asia and Africa. Amongmariner elements in species within and outside theDrosophilidae, the similarities in nucleotide sequence and the amino acid sequence of the putative transposase reveal many phylogenetic inconsistencies compared with the conventional phylogeny of the host species. This paper discusses the contrasting hypotheses of horizontal transfer versus ancestral origin proposed to explain these results.