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1.
Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic
genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between
the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous
homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively
referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the
structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a
tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence
analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences
suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral
provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the
orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human,
chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13
family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.
Received: 29 September 1997 / Accepted: 16 January 1998 相似文献
2.
Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one
or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual,
highly conserved, elements of the B1 SINE family were identified from the GenBank nucleotide database using various B1 subfamily
consensus query sequences to determine their integration times into the mouse genome. A comparison of orthologous loci in
various species of the genus Mus demonstrated that four subfamilies of B1 elements have been amplifying within the last 1–3 million years. Therefore, B1 sequences
are generated by coexisting source genes. Additionally, three B1 subfamilies have been concurrently propagated during subspecies
divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patterns of intra- and interspecies variations of orthologous
loci demonstrate the usefulness of B1 integrations as a phylogenetic tool. A single inconsistency in the phylogenetic trends
was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved
B1 element that integrated at least 4–6 million years ago suggests the possibility of occasional function for B1 integrations.
Received: 25 February 2000 / Accepted: 5 June 2000 相似文献
3.
The increasing amount of data generated in recent years has opened the way to exhaustive studies of the relationships among
different members of the Ty3/gypsy group of LTR retrotransposons, a widespread group of eukaryotic transposable elements. Former research led to the identification
of several independent lineages within this group. One of the worse represented of them is that of mdg1, integrated so far only by the Drosophila retrotransposons mdg1 and 412. Our exhaustive database searches indicate the existence of three other Drosophila members of this lineage. Two of them correspond to elements already known, namely, Stalker and blood, but the third one is a new element, which we have called Pilgrim. This element is well represented within the D. melanogaster genome, as revealed by our Southern blot analysis of different strains. The case of Stalker is particularly remarkable, since its phylogenetic relationships clearly point to the mosaic origin of its genome. Finally,
our analysis of the evolution of a small ORF preserved within the 5′ leader region of these elements indicates different evolutionary
rates, presumably as a result of distinct selective constraints.
Received: 16 October 2000 / Accepted: 6 April 2001 相似文献
4.
The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons
residing within a single genome. In this article we report the results of such an analysis of two closely related families
of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing
among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family
is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein
coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event
has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological
significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon
evolution.
Received: 30 September 1997 / Accepted: 3 February 1998 相似文献
5.
We present here the sequence and characterization of various minisatellite-like tandem repeat loci isolated from the genome
of Atlantic salmon (Salmo salar). Their diversity of sequence and lack of core motifs common to minisatellites of other species suggest the presence of numerous
and previously unidentified simple sequence repeat families in this salmonid. Evidence for their ubiquity was provided by
screening of a salmon genomic library. Southern blot analysis of the phylogenetic distribution of a subset of the minisatellites
found one sequence to be pervasive among vertebrates, others present only in Salmoninae or Salmonidae species, and one amplified
only in Atlantic salmon. There is evidence for the positioning of microsatellite and minisatellite arrays in close proximity
at many loci. Furthermore, one tandem repeat appears to have been inserted into the transposase coding region of a copy of
the Tc1 transposon-like element recently identified in salmonids.
Received: 9 October 1996 / Accepted: 20 May 1997 相似文献
6.
7.
A family of four satellite DNAs has been characterized in the genome of the bivalve mollusc, Donax trunculus. All share HindIII sites, a similar monomer length of about 160 base pairs (bp), and the related oligonucleotide motifs GGTCA and GGGTTA,
repeated six to 15 times within the repetitive units. The motif GGTCA is common to all members of the satellite family. It
is present in three of them in both orientations, interspersed within nonrepetitive DNA sequences. The hexanucleotide GGGTTA
appears to be the main building element of one of the satellites forming a prominent subrepeat structure in conjunction with
the 5-bp motif. The former has been also found in perfect tandem repeats in a junction region adjacent to the proper satellite
sequence. Southern analysis has revealed that (GGGTTA)n and/or related sequences are abundant and widely distributed in the D. trunculus genome. The distribution observed is consistent with the concurrence of the scattering of short sequence motifs throughout
the genome and the spread of longer DNA segments, with concomitant formation of satellite monomer repeats. Both kinds of dispersion
may have contributed to the observed complex arrangement of the HindIII satellite DNA family in Donax.
Received: 28 May 1996 / Accepted: 30 July 1996 相似文献
8.
R. Kalendar T. Grob M. Regina A. Suoniemi A. Schulman 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(5):704-711
The BARE-1 retrotransposon is an active, dispersed, and highly abundant component of the genome of barley (Hordeum vulgare) and other species in its genus. Like all retrotransposons of its kind, BARE-1 is bounded by long terminal repeats (LTRs). We have developed two amplification-based marker methods based on the position
of given LTRs within the genome. The IRAP (Inter-Retrotransposon Amplified Polymorphism) markers are generated by the proximity of two LTRs using outward-facing primers annealing to LTR target sequences.
In REMAP (REtrotransposon-Microsatellite Amplified Polymorphism), amplification between LTRs proximal to simple sequence repeats such as constitute microsatellites produces markers.
The methods can distinguish between barley varieties and produce fingerprint patterns for species across the genus. The patterns
indicate that although the BARE-1 family of retrotransposons is disperse, these elements are locally clustered or nested and often found near tandem arrays
of a simple sequence repeat.
Received: 30 June 1998 / Accepted: 21 August 1998 相似文献
9.
RETROTRANSPOSON MYS IS CONCENTRATED ON THE SEX CHROMOSOMES: IMPLICATIONS FOR COPY NUMBER CONTAINMENT
Robert J. Baker Holly A. Wichman 《Evolution; international journal of organic evolution》1990,44(8):2083-2088
Chromosomal distribution of the mys retrotransposon was examined by in situ hybridization with a biotinylated probe. Thirty-six mice from four species of the Peromyscus leucopus/maniculatus complex were examined. Mys hybridized to every chromosome in all individuals examined. However, the pattern of hybridization was nonrandom. Mys elements were excluded from C-banding regions of the autosomes, and hybridized preferentially to G-bands. The most prominent feature of these hybridizations was the preferential accumulation of mys on the X and Y chromosomes of all four species examined. Accumulation of mys on the X is incompatible with the hypothesis that selection acting on deleterious mutations is the major mechanism regulating the copy number of this element. Rather, this supports the Langley model for containment of transposable element copy number by unequal exchange during meiosis. 相似文献
10.
M.D. Moltó N. Paricio M.A. López-Preciado V.F. Semeshin M.J. Martínez-Sebastián 《Journal of molecular evolution》1996,42(3):369-375
In this paper we report a new retrotransposon-like element of Drosophila melanogaster called Tirant. This sequence is moderately repeated in the genome of this species and it has been found to be widely dispersed throughout
its distribution area. From Southern blot and in situ analyses, this sequence appears to be mobile in D. melanogaster, since its chromosome location and the hybridization patterns vary among the different strains analyzed. In this way, partial
sequencing of Tirant ends suggests that it is a retrotransposon, since it is flanked by two LTRs. The presence of sequences homologous to Tirant has been also investigated in 28 species of the genus Drosophila by means of Southern analyses. These sequences were only detected in species from melanogaster and obscura groups. These data suggest that ancestral sequences of Tirant appeared after the Sophophora radiation and before the divergence of those groups.
Received: 1 January 1995 / Accepted: 20 August 1995 相似文献
11.
Short Retroposons of the B2 Superfamily: Evolution and Application for the Study of Rodent Phylogeny
Short retroposons can be used as natural phylogenetic markers. By means of hybridization and PCR analysis, we demonstrate
that B2 retroposon copies are present only in the three rodent families: Muridae, Cricetidae, and Spalacidae. This observation
highlights the close phylogenetic relation between these families. Two novel B2-related retroposon families, named DIP and
MEN elements, are described. DIP elements are found only in the genomes of jerboas (family Dipodidae) and birch mice (family
Zapodidae), demonstrating the close relationship between these rodents. MEN element copies were isolated from the squirrel,
Menetes berdmorei, but were not detected in three other species from the family Sciuridae. The MEN element has an unusual dimeric structure:
the left and right monomers are B2- and B1-related sequences, respectively. Comparison of the B2, DIP, MEN, and 4.5S1 RNA elements revealed an 80-bp core sequence located at the beginning of the B2 superfamily retroposons. This observation
suggests that these retroposon families descended from a common progenitor. A likely candidate for this direct progenitor
could be the ID retroposon.
Received: 20 December 1996 / Accepted: 17 June 1997 相似文献
12.
Kazuhiko Takahashi Mutsumi Nishida Masahide Yuma Norihiro Okada 《Journal of molecular evolution》2001,53(4-5):496-507
Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation.
To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed
repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically
inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another
locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with
the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating
that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized
a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna
species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be
occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular
when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.
Received: 15 December 2000 / Accepted: 30 January 2001 相似文献
13.
14.
Isaäc J. Nijman Patrick van Tessel Johannes A. Lenstra 《Journal of molecular evolution》2002,54(1):9-16
SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic
levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points
of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions
in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked
by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA
insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation
of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant α-lactalbumine
gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion.
Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition
was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of
SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of
SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions
of ruminants.
Received: 19 January 2001 / Accepted: 6 June 2001 相似文献
15.
We report the results of an analysis of naturally occurring cis-regulatory variation within and between two families of the
copia Drosophila long terminal repeat (LTR) retrotransposon. The copia 5′ LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play
a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for
generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide variation and subjected the data to a series of tests of neutrality. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within families and positive adaptive selection between families.
We discuss these findings with respect to the regulatory evolution of retrotransposons and the phenomenon of interelement
selection.
Received: 5 February 1998 / Accepted: 14 May 1998 相似文献
16.
Although bacterial species display wide variation in their overall GC contents, the genes within a particular species' genome
are relatively similar in base composition. As a result, sequences that are novel to a bacterial genome—i.e., DNA introduced
through recent horizontal transfer—often bear unusual sequence characteristics and can be distinguished from ancestral DNA.
At the time of introgression, horizontally transferred genes reflect the base composition of the donor genome; but, over time,
these sequences will ameliorate to reflect the DNA composition of the new genome because the introgressed genes are subject
to the same mutational processes affecting all genes in the recipient genome. This process of amelioration is evident in a
large group of genes involved in host-cell invasion by enteric bacteria and can be modeled to predict the amount of time required
after transfer for foreign DNA to resemble native DNA. Furthermore, models of amelioration can be used to estimate the time
of introgression of foreign genes in a chromosome. Applying this approach to a 1.43-megabase continuous sequence, we have
calculated that the entire Escherichia coli chromosome contains more than 600 kb of horizontally transferred, protein-coding DNA. Estimates of amelioration times indicate
that this DNA has accumulated at a rate of 31 kb per million years, which is on the order of the amount of variant DNA introduced
by point mutations. This rate predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence.
Received: 7 July 1996 / Accepted: 27 September 1996 相似文献
17.
Evolution of Duplicated <Emphasis Type="BoldItalic">reggie</Emphasis> Genes in Zebrafish and Goldfish 总被引:1,自引:0,他引:1
Málaga-Trillo E Laessing U Lang DM Meyer A Stuermer CA 《Journal of molecular evolution》2002,54(2):235-245
Invertebrates, tetrapod vertebrates, and fish might be expected to differ in their number of gene copies, possibly due the
occurrence of genome duplication events during animal evolution. Reggie (flotillin) genes code for membrane-associated proteins involved in growth signaling in developing and regenerating axons. Until now,
there appeared to be only two reggie genes in fruitflies, mammals, and fish. The aim of this research was to search for additional copies of reggie genes in fishes, since a genome duplication might have increased the gene copy number in this group. We report the presence
of up to four distinct reggie genes (two reggie-1 and two reggie-2 genes) in the genomes of zebrafish and goldfish. Phylogenetic analyses show that the zebrafish and goldfish sequence pairs
are orthologous, and that the additional copies could have arisen through a genome duplication in a common ancestor of bony
fish. The presence of novel reggie mRNAs in fish embryos indicates that the newly discovered gene copies are transcribed and possibly expressed in the developing
and regenerating nervous system. The intron/exon boundaries of the new fish genes characterized here correspond with those
of human genes, both in location and phase. An evolutionary scenario for the evolution of reggie intron-exon structure, where loss of introns appears to be a distinctive trait in invertebrate reggie genes, is presented.
Received: 24 January 2001 / Accepted: 27 July 2001 相似文献
18.
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20.
Sybille Kubis John Seymour Heslop-Harrison Thomas Schmidt 《Journal of molecular evolution》1997,44(3):310-320
Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size
variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative
study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species
was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within
and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization
to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection
of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies.
Received: 24 May 1996 / Accepted: 13 September 1996 相似文献