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1.
Vertical Transmission of the Retrotransposable Elements R1 and R2 during the Evolution of the Drosophila Melanogaster Species Subgroup 总被引:2,自引:0,他引:2
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. 相似文献
2.
A single lineage of r2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus 总被引:1,自引:0,他引:1
R2 elements are non-long-terminal-repeat (non-LTR) retrotransposons that
insert specifically in the 28S rRNA genes of many insects. Previous reports
concerning this element in the genus Drosophila have suggested that R2
elements are absent from many species of this genus, particularly those
species from the subgenus Drosophila. In this report, we present an
extensive study of the distribution and evolution of R2 elements in
Drosophila. A PCR survey of 59 species from 23 species groups of the two
major Drosophila subgenera found that R2 elements are present in all but
two species of the melanogaster species subgroup. Phylogenetic analysis
based on partial nucleotide sequences of R2 elements from 23 species
demonstrates that the relationships of R2 elements are congruent with those
of the Drosophila species phylogeny, suggesting that these elements have
been vertically inherited since the divergence of this genus some 60 MYA.
Sequence variation between different copies of R2 elements within each
species was less than 0.16%, indicating that these elements are undergoing
concerted evolution similar to that of the 28S genes. Several properties of
the R2 sequences suggest that these elements depend on retrotransposition
in addition to simple recombination to remain within the rDNA locus: the
rates of synonymous substitutions averaged 4.8 times the rate of
replacement substitutions, 82 of 83 R2 copies partially sequenced contained
intact open reading frames, and, finally, length variation associated with
the poly(A) 3' tails indicated that many R2 copies are the direct result of
retrotransposition.
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3.
In Situ Hybridization Analysis of Chromosomal Homologies in Drosophila Melanogaster and Drosophila Virilis 总被引:4,自引:3,他引:1
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Twenty-four biotin-labeled recombinant-DNA probes which contained putative unique-sequence Drosophila melanogaster DNA were hybridized to larval salivary-gland chromosomes of D. melanogaster and Drosophila virilis. All probes hybridized to D. melanogaster chromosomes at the expected sites. However, one probe hybridized to at least 16 additional sites, and one hybridized to one additional site. Thirteen probes hybridized strongly to D. virilis chromosomes, four hybridized weakly and infrequently, and seven did not hybridize. Probes representing two multigene families (beta-tubulin and yolk-protein) hybridized as would be expected if all sites had been conserved in the two species on the same chromosomal elements. The multiple hybridization sites of a third probe which may represent a multigene family were also conserved. The results were consistent with H.J. Muller's proposal that chromosomal elements have been conserved during evolution of this genus. 相似文献
4.
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. 相似文献
5.
The maintenance of the telomeres in Drosophila species depends on the transposition of the non-LTR retrotransposons HeT-A, TAHRE and TART. HeT-A and TART elements have been found in all studied species of Drosophila suggesting that their function has been maintained for more than 60 million years. Of the three elements, HeT-A is by far the main component of D. melanogaster telomeres and, unexpectedly for an element with an essential role in telomere elongation, the conservation of the nucleotide sequence of HeT-A is very low. In order to better understand the function of this telomeric retrotransposon, we studied the degree of conservation along HeT-A copies. We identified a small sequence within the 3' UTR of the element that is extremely conserved among copies of the element both, within D. melanogaster and related species from the melanogaster group. The sequence corresponds to a piRNA target in D. melanogaster that we named HeT-A_pi1. Comparison with piRNA target sequences from other Drosophila retrotransposons showed that HeT-A_pi1 is the piRNA target in the Drosophila genome with the highest degree of conservation among species from the melanogaster group. The high conservation of this piRNA target in contrast with the surrounding sequence, suggests an important function of the HeT-A_pi1 sequence in the co-evolution of the HeT-A retrotransposon and the Drosophila genome. 相似文献
6.
Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. 总被引:58,自引:0,他引:58
The stability of elements of three different dispersed repeated gene families in the genome of Drosophila tissue culture cells has been examined. Different amounts of sequences homologous to elements of 412, copia and 297 dispersed repeated gene families are found in the genomes of D. melanogaster embryonic and tissue culture cells. In general the amount of these sequences is increased in the cell lines. The additional sequences homologous to 412, copia and 297 occur as intact elements and are dispersed to new sites in the cell culture genome. It appears that these elements can insert at many alternative sites. We also describe a DNA sequence arrangement found in the D. melanogaster embryo genome which appears to result from a transposition of an element of the copia dispersed repeated gene family into a new chromosomal site. The mechanism of insertion of this copia element is precise to within 90 bp and may involve a region of weak sequence homology between the site of insertion and the direct terminal repeats of the copia element. 相似文献
7.
8.
Distribution and conservation of sequences homologous to the 1731 retrotransposon in Drosophila 总被引:3,自引:1,他引:2
Montchamp-Moreau C; Ronsseray S; Jacques M; Lehmann M; Anxolabehere D 《Molecular biology and evolution》1993,10(4):791-803
The distribution of 1731 retrotransposon-hybridizing sequences in the
family Drosophilidae has been studied using a 1731 probe from Drosophila
melanogaster. Squash blot and Southern blot analyses of 42 species reveal
that the 1731 sequences are widespread within both the Sophophora and
Drosophila subgenera and are also present in the genera Scaptomyza and
Zaprionus. Hence the 1731 retrotransposon family appears to have a long
evolutionary history in the Drosophilidae genome. Differences of
hybridization signal intensity suggested that the 1731 sequence is well
conserved only in the three species most closely related to D. melanogaster
(D. simulans, D. mauritiana, and D. sechellia). A survey of insertion sites
in numerous different populations of the previous four species by in situ
hybridization to polytene chromosomes has shown in all cases both
chromocentric hybridizations and a low number of sites (0-5) on the
chromosomal arms. This number of sites is among the lowest observed in D.
melanogaster and D. simulans when 1731 is compared with other
retrotransposon families. In addition, we have observed species-specific
patterns of the chromocentric hybridization signal, suggesting rapid
modifications of the beta-heterochromatin components since the radiation of
the melanogaster subgroup.
相似文献
9.
Recent results indicate that the rate of chromosomal rearrangement in the genus Drosophila is the highest found so far in any eukaryote. This conclusion is based chiefly on the comparative mapping analysis of a single chromosomal element (Muller's element E) in two species, D. melanogaster and D. repleta, representing the two farthest lineages within the genus (the Sophophora and Drosophila subgenera, respectively). We have extended the analysis to two other chromosomal elements (Muller's elements A and D) and tested for differences in rate of evolution among chromosomes. With this purpose, detailed physical maps of chromosomes X and 4 of D. repleta were constructed by in situ hybridization of 145 DNA probes (gene clones, cosmids, and P1 phages) and their gene arrangements compared with those of the homologous chromosomes X and 3L of D. melanogaster. Both chromosomal elements have been extensively reshuffled over their entire length. The number of paracentric inversions fixed has been estimated as 118 +/- 17 for element A and 56 +/- 8 for element D. Comparison with previous data for elements E and B shows that there are fourfold differences in evolution rate among chromosomal elements, with chromosome X exhibiting the highest rate of rearrangement. Combining all results, we estimated that 393 paracentric inversions have been fixed in the whole genome since the divergence between D. repleta and D. melanogaster. This amounts to an average rate of 0.053 disruptions/Mb/myr, corroborating the high rate of rearrangement in the genus Drosophila. 相似文献
10.
Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA 总被引:2,自引:0,他引:2
The long (4.6-kb) A+T region of Drosophila melanogaster mitochondrial DNA
has been cloned and sequenced. The A+T region is organized in two large
arrays of tandemly repeated DNA sequence elements, with nonrepetitive
intervening and flanking sequences comprising only 22% of its length. The
first repeat array consists of five repeats of 338-373 bp. The second
consists of four intact 464-bp repeats and a fifth partial repeat of 137
bp. Three DNA sequence elements are found to be highly conserved in D.
melanogaster and in several Drosophila species with short A+T regions.
These include a 300-bp DNA sequence element that overlaps the DNA
replication origin and two thymidylate stretches identified on opposite DNA
strands. We conclude that the length heterogeneity observed in the A+T
regulatory region in mitochondrial DNAs from the genus Drosophila results
from the expansion (and contraction) of the number of repeated DNA sequence
elements. We also propose that the 300-bp conserved DNA sequence element,
in conjunction with another primary sequence determinant, perhaps the
adjacent thymidylate stretch, functions in the regulation of mitochondrial
DNA replication.
相似文献
11.
Evidence for Horizontal Transmission of the P Transposable Element between Drosophila Species 总被引:17,自引:7,他引:10
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S. B. Daniels K. R. Peterson L. D. Strausbaugh M. G. Kidwell A. Chovnick 《Genetics》1990,124(2):339-355
Several studies have suggested that P elements have rapidly spread through natural populations of Drosophila melanogaster within the last four decades. This observation, together with the observation that P elements are absent in the other species of the melanogaster subgroup, has lead to the suggestion that P elements may have entered the D. melanogaster genome by horizontal transmission from some more distantly related species. In an effort to identify the potential donor in the horizontal transfer event, we have undertaken an extensive survey of the genus Drosophila using Southern blot analysis. The results showed that P-homologous sequences are essentially confined to the subgenus Sophophora. The strongest P hybridization occurs in species from the closely related willistoni group. A wild-derived strain of D. willistoni was subsequently selected for a more comprehensive molecular examination. As part of the analysis, a complete P element was cloned and sequenced from this line. Its nucleotide sequence was found to be identical to the D. melanogaster canonical P, with the exception of a single base substitution at position 32. When the cloned element was injected into D. melanogaster embryos, it was able to both promote transposition of a coinjected marked transposon and induce singed-weak mutability, thus demonstrating its ability to function as an autonomous element. The results of this study suggest that D. willistoni may have served as the donor species in the horizontal transfer of P elements to D. melanogaster. 相似文献
12.
E Strobel 《Federation proceedings》1982,41(10):2656-2658
The molecular and cytogenetic organizations of 19 nonhomologous dispersed repeated sequence families were studied in 15 different laboratory strains of Drosophila melanogaster. Elements from each of the families appear to undergo transposition within the Drosophila genome, because there were striking differences in both the number and chromosomal locations of these elements between strains. A significant fraction (greater than 1%) of Drosophila DNA therefore has an unstable genomic organization. Each middle repetitive family exhibited similar variations in the chromosomal distribution of elements between the strains. Although the movements of these elements are not limited to a small number of genomic sites, there are chromosomal regions where elements from the different dispersed repeated DNA families appear to be clustered. The locations of such preferred integration sites are different in each of the D. melanogaster strains examined. 相似文献
13.
S Elements: A Family of Tc1-like Transposons in the Genome of Drosophila Melanogaster 总被引:2,自引:0,他引:2
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P. J. Merriman C. D. Grimes J. Ambroziak D. A. Hackett P. Skinner M. J. Simmons 《Genetics》1995,141(4):1425-1438
The S elements form a diverse family of long-inverted-repeat transposons within the genome of Drosophila melanogaster. These elements vary in size and sequence, the longest consisting of 1736 bp with 234-bp inverted terminal repeats. The longest open reading frame in an intact S element could encode a 345-amino acid polypeptide. This polypeptide is homologous to the transposases of the mariner-Tc1 superfamily of transposable elements. S elements are ubiquitous in D. melanogaster populations and also appear to be present in the genomes of two sibling species; however, they seem to be absent from 17 other Drosophila species that were examined. Within D. melanogaster strains, there are, on average, 37.4 cytologically detectable S elements per diploid genome. These elements are scattered throughout the chromosomes, but several sites in both the euchromatin and β heterochromatin are consistently occupied. The discovery of an S-element-insertion mutation and a reversion of this mutation indicates that S elements are at least occasionally mobile in the D. melanogaster genome. These elements seem to insert at an AT dinucleotide within a short palindrome and apparently duplicate that dinucleotide upon insertion. 相似文献
14.
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. 相似文献
15.
D Anxolabehere 《Comptes rendus des séances de la Société de biologie et de ses filiales》1992,186(6):641-655
The P transposable element family in Drosophila melanogaster is responsible for the syndrome of hybrid dysgenesis which includes chromosomal rearrangements, male recombination, high mutability and temperature sensitive agametic sterility (called gonadal dysgenesis sterility). P element activity is controlled by a complex regulation system, encoded by the elements themselves, which keeps their transposition rate low within the strain bearing P elements and limits copy number by genome. A second regulatory mechanism, which acts on the level of RNA processing, prevents P mobility to somatic cells. The oldest available strains, representing most major geographical regions of the world, exhibited no detectable hybridization to the P-element. In contrast, all recently collected natural populations that were tested carried P-element sequences. The available evidence is consistent with the hypothesis of a worldwide P-element invasion of D. melanogaster during the past 30 years. Timing and direction of the invasion are discussed. The lack of P-element in older strains of Drosophila melanogaster as well as in the species must closely related to Drosophila melanogaster, suggests that P entered the Drosophila melanogaster genome recently, probably by horizontal transfer from an other species. The analysis of P-element elsewhere in the genus Drosophila reveals that several more distantly related species carried transposable elements with sequences quite similar to P. The species with the best-matching P-element is D. willistoni. A P-element from this species was found to match all but one of the 2907 nucleotides of the Drosophila melanogaster P-element. The phylogenic distributions and the likely horizontal transfers of the two other Drosophila transposable elements are discussed. 相似文献
16.
G M Simmons 《Molecular biology and evolution》1992,9(6):1050-1060
The hobo family of transposable elements, one of three transposable-element families that cause hybrid dysgenesis in Drosophila melanogaster, appears to be present in all members of the D. melanogaster species complex: D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. Some hobo-hybridizing sequences are also found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older isofemale lines of D. melanogaster suggest that complete hobo elements were absent prior to 50 years ago and that hobo has recently been introduced into the species by horizontal transfer. To test the horizontal transfer hypothesis, the 2.6-kb XhoI fragments of hobo elements from D. melanogaster, D. simulans, and D. mauritiana were cloned and sequenced. The DNA sequences reveal an extremely low level of divergence and support the conclusion that the active hobo element has been horizontally transferred into or among these species in the recent past. 相似文献
17.
The non-LTR retrotransposons R1 and R2 insert into the 28S rRNA genes of arthropods. Comparisons among Drosophila lineages have shown that these elements are vertically inherited, while studies within species have indicated a rapid turnover of individual copies (elimination of old copies and the insertion of new copies). To better understand the turnover of R1 and R2, 200 retrotranspositions and nearly 100 eliminations have been scored in the Harwich mutation-accumulation lines of Drosophila melanogaster. Because the rDNA arrays in D. melanogaster are present on the X and Y chromosomes and no exchanges were detected in these lines, it was possible to show that R1 retrotranspositions occur predominantly in the male germ line, while R2 retrotranspositions were more evenly divided between the germ lines of both sexes. The rate of elimination of elements from the Y rDNA array was twice that of the X rDNA array with both chromosomal loci containing regions where the rate of elimination was on average eight times higher. Most R1 and R2 eliminations appear to occur by large intrachromosomal events (i.e., loop-out events) that involve multiple rDNA units. These findings are interpreted in light of the known abundance of R1 and R2 elements in the X and Y rDNA loci of D. melanogaster. 相似文献
18.
Thomas H. Eickbush William D. Burke Danna G. Eickbush Warren C. Lathe III 《Genetica》1997,100(1-3):49-61
R1 and R2 are non-long terminal repeat (non-LTR) retrotransposable elements that specifically insert in the 28S ribosomal
RNA (rRNA) genes of insects. Using the Drosophila genus, which includes some of the best characterized insect taxa, we have
conducted a number of studies on the evolution of these elements. We find that R1 and R2 are subject to the same recombinational
forces that give rise to the concerted evolution of the rDNA units. The turnover of R1 and R2 elements can be readily documented
in different strains of D. melanogaster using 5′ truncated elements as restriction-length polymorphisms. This turnover leads
to uniform populations of elements with nucleotide sequence divergence of different copies averaging only 0.23% for the R2
and 0.47% for the R1 elements. Molecular phylogenetic analysis of elements from 16 different species of Drosophila suggests
that these elements have been stable components of the rDNA locus for the 50–70 million year history of the Drosophila genus.
Using changes at synonymous positions within the protein-encoding regions as estimates of the baseline substitution rate,
it could be shown that R1 and R2 are evolving at rates similar to that of typical protein encoding genes provided corrections
are made for the low codon bias of the elements. R1 and R2 are clearly well-adapted for their existence in the rDNA units
of their host.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
19.
The mobile element ZAM, recently identified in Drosophila melanogaster, is similar in structure and coding potential to vertebrate
retroviruses. In this paper, we analyze the insertional and structural polymorphism of this element and show that members
of this family appear to have a long evolutionary history in the genome of Drosophila. It is present in all the species of
the D. melanogaster subgroup and in more distantly related species like D. takahashii, D. ananassae, or D. virilis but in
a lower copy number or with a lower homology. Two categories of strains have been previously identified in D. melanogaster:
strains with a high copy number of ZAM and strains with a low copy number. Here, we show that ZAM is at least in a low copy
number in each tested strain of the species analyzed. The study of ZAM's genomic distribution by FISH mapping analysis to
salivary gland polytene chromosomes or on mitotic chromosomes indicates that most of the insertion sites of ZAM elements are
associated with the constitutive heterochromatin regardless of the ZAM copy number. In addition, our results suggest that
multiple ZAM elements are present at the insertion sites visualized by in situ experiments.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献