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1.
The intriguing diversity of highly abundant satellite repeats found even among closely related species can result from processes
leading to dramatic changes in copy number of a particular sequence in the genome and not from rapid accumulation of mutations.
To test this hypothesis, we investigated the distribution of the PRAT satellite DNA family, a highly abundant major satellite
in the coleopteran species Palorus ratzeburgii, in eight species belonging to the related genera (Tribolium, Tenebrio, Latheticus), the subfamily (Pimeliinae), and the family (Chrysomelidae). Dot blot analysis and PCR assay followed by Southern hybridization
revealed that the PRAT satellite, in the form of low-copy number repeats, was present in all tested species. The PRAT satellite
detected in the species Pimelia elevata has been sequenced, and compared with previously cloned PRAT monomers from Palorus ratzeburgii and Palorus subdepressus. Although the two Palorus species diverged at least 7 Myr ago, and the subfamily Pimeliinae separated from the genus Palorus 50–60 Myr ago, all PRAT clones exhibit high mutual homology, with average variability relative to the common consensus sequence
of 1.3%. The presence of ancestral mutations found in PRAT clones from all three species as well as the absence of species
diagnostic mutations illustrate extremely slow sequence evolution. This unexpectedly high conservation of PRAT satellite DNA
sequence might be induced by a small bias of turnover mechanisms favoring the ancestral sequence in the process of molecular
drive. 相似文献
2.
Mutation and Recombination in Cattle Satellite DNA: A Feedback Model for the Evolution of Satellite DNA Repeats 总被引:6,自引:0,他引:6
The cattle genome contains several distinct centromeric satellites with interrelated evolutionary histories. We compared
these satellites in Bovini species that diverged 0.2 to about 5 Myr ago. Quantification of hybridization signals by phosphor imaging revealed a large
variation in the relative amounts of the major satellites. In the genome of water buffalo this has led to the complete deletion
of satellite III. Comparative sequencing and PCR-RFLP analysis of satellites IV, 1.711a, and 1.711b from the related Bos and Bison species revealed heterogeneities in 0.5 to 2% of the positions, again with variations in the relative amounts of sequence
variants. Restriction patterns generated by double digestions suggested a recombination of sequence variants. Our results
are compatible with a model of the life history of satellites during which homogeneity of interacting repeat units is both
cause and consequence of the rapid turnover of satellite DNA. Initially, a positive feedback loop leads to a rapid saltatory
amplification of homogeneous repeat units. In the second phase, mutations inhibit the interaction of repeat units and coexisting
sequence variants amplify independently. Homogenization by the spreading of one of the variants is prevented by recombination
and the satellite is eventually outcompeted by another, more homogeneous tandem repeat sequence.
Received: 21 July 2000 / Accepted: 30 October 2000 相似文献
3.
4.
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
5.
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
6.
7.
Due to a high evolutionary turnover many satellite DNAs are restricted to a group of closely related species. Here we demonstrate
that the satellite DNA family PSUB, abundant in the beetle Palorus subdepressus, is distributed in a low number of copies among diverse taxa of Coleoptera (Insecta), some of them separated for an evolutionary
period of up to 60 Myr. Comparison of PSUB cloned from the species Tribolium brevicornis with the PSUB family previously characterized in Palorus subdepressus revealed high sequence conservation and absence of fixed species-specific mutations. The most polymorphic sites are those
with ancestral mutations shared among clones of both species. Since the ancestral mutations contribute significantly to overall
diversity, it could be proposed that a similar mutational profile already existed in an ancestral species. The pattern of
variability along the satellite monomer is characterized by the presence of conserved and variable regions. The nonrandom
pattern of variability as well as the absence of sequence divergence is also discerned for PRAT satellite DNA, cloned previously
from two Palorus species and a distantly related Pimelia elevata. Since PRAT and PSUB are present in parallel in diverse taxa of Coleoptera, we propose that their long evolutionary preservation
suggests a possible functional significance. This indication is additionally supported not only by the high evolutionary conservation
of the sequences, but also by the presence of significantly conserved and variable regions along the monomers.
[Reviewing Editor: Dr. Jerzy Jurka] 相似文献
8.
A PstI DNA family was isolated from the genome of a lacertid, Lacerta graeca. The 185-bp monomeric unit (pGPS) was cloned and hybridized to DNAs and chromosomes of several lacertid species. The data
showed that pGPS hybridizes to the (1) centromeric or pericentromeric heterochromatin of almost all the chromosomes of L. graeca and (2) genomic DNA of species phylogenetically related and unrelated to L. graeca. The presence of pGPS even in species immunologically apart more than 30 million years suggests that this repeated family
might be either very ancient or have been conserved during evolution due to its functional role. The latter hypothesis might
be supported by the results of sequence analysis which showed some homology with both several alphoid sequences of primates
and the CDEIII centromeric sequence of yeast. Segments of the satellite sequence are similar to the mammalian CENP-B box.
These observations suggest that pGPS might have a role in determining the centromeric function in lacertid lizards.
Received: 6 February 1997 / Accepted: 14 May 1997 相似文献
9.
This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish
and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes
cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located
in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by
polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were
determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the
length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination
of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of
both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this
multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate
DNA sequence for comparisons of closely related taxa.
Received: 22 August 1997 / Accepted: 31 October 1997 相似文献
10.
Charles Lee Dean R. Court Charles Cho Jennifer L. Haslett Chyi-Chyang Lin 《Journal of molecular evolution》1997,44(3):327-335
Based on sequence analyses of 17 complete centromeric DNA monomers from ten different deer species, a model is proposed for
the genesis, evolution, and genomic organization of cervid satellite I DNA. All cervid satellite I DNA arose from the initial
amplification of a 31-bp DNA sequence. These 31-bp subrepeats were organized in a hierarchical fashion as 0.8-kb monomers
in plesiometacarpalia deer and 1-kb monomers in telemetacarpalia deer. The higher-order repeat nature of cervid centromeric
satellite DNA monomers accounts for their high intragenomic and intraspecific sequence conservation. Such high intraspecific
sequence conservation validates the use of a single cervid satellite I DNA monomer from each deer species for interspecific
sequence comparisons to elucidate phylogenetic relationships. Also, a specific 0.18-kb tandem duplication was observed in
all 1-kb monomers, implying that 1-kb cervid satellite I DNA monomers arose from an unequal crossover event between two similar
0.8-kb ancestral DNA sequences.
Received: 28 May 1996 / Accepted: 24 October 1996 相似文献
11.
Philippe Castagnone-Sereno Hélène Leroy Jean-Philippe Semblat Frédéric Leroy Pierre Abad Carolien Zijlstra 《Journal of molecular evolution》1998,46(2):225-233
An AluI satellite DNA family has been isolated in the genome of the root-knot nematode Meloidogyne chitwoodi. This repeated sequence was shown to be present at approximately 11,400 copies per haploid genome, and represents about 3.5%
of the total genomic DNA. Nineteen monomers were cloned and sequenced. Their length ranged from 142 to 180 bp, and their A
+ T content was high (from 65.7 to 79.1%), with frequent runs of As and Ts. An unexpected heterogeneity in primary structure
was observed between monomers, and multiple alignment analysis showed that the 19 repeats could be unambiguously clustered
in six subfamilies. A consensus sequence has been deduced for each subfamily, within which the number of positions conserved
is very high, ranging from 86.7% to 98.6%. Even though blocks of conserved regions could be observed, multiple alignment of
the six consensus sequences did not enable the establishment of a general unambiguous consensus sequence. Screening of the
six consensus sequences for evidence of internal repeated subunits revealed a 6-bp motif (AAATTT), present in both direct
and inverted orientation. This motif was found up to nine times in the consensus sequences, also with the occurrence of degenerated
subrepeats. Along with the meiotic parthenogenetic mode of reproduction of this nematode, such structural features may argue
for the evolution of this satellite DNA family either (1) from a common ancestral sequence by amplification followed by mechanisms
of sequence divergence, or (2) through independent mutations of the ancestral sequence in isolated amphimictic nematode populations
and subsequent hybridization events. Overall, our results suggest the ancient origin of this satellite DNA family, and may
reflect for M. chitwoodi a phylogenetic position close to the ancestral amphimictic forms of root-knot nematodes.
Received: 23 April 1997 / Accepted: 9 July 1997 相似文献
12.
Chromosome terminal, complex repeats in the dipteran Chironomus pallidivittatus show rapid concerted evolution during which there is remarkably efficient homogenization of the repeat units within and between
chromosome ends. It has been shown previously that gene conversion is likely to be an important component during these changes.
The sequence evolution could be a result of different processes—exchanges between repeats in the tandem array as well as information
transfer between units in different chromosomes—and is therefore difficult to analyze in detail. In this study the concerted
evolution of a region present only once per chromosome, at the junction between the telomeric complex repeats and the subtelomeric
DNA was therefore investigated in the two sibling species C. pallidivittatus and C. tentans. Material from individual microdissected chromosome ends was used, as well as clones from bulk genomic DNA. On the telomeric
side of the border pronounced species-specific sequence differences were observed, the patterns being similar for clones of
different origin within each species. Mutations had been transmitted efficiently between chromosomes also when adjoining,
more distally localized DNA showed great differences in sequence, suggesting that gene conversion had taken place. The evolving
telomeric region bordered proximally to subtelomeric DNA with high evolutionary constancy. More proximally localized, subtelomeric
DNA evolved more rapidly and showed heterogeneity between species and chromosomes.
Received: 24 September 1997 / Accepted: 24 November 1997 相似文献
13.
To date, the small nuclear 4.5SI RNA has only been studied in the rat (Rattus norvegicus). Combining PCR and hybridization analyses, we have revealed 4.5SI RNA homologues sequences in the genomes of four myomorph rodent families (Muridae, Cricetidae, Spalicidae, and Rhizomyidae),
and not in other myomorph families (Dipodidae, Zapodidae, Geomyidae, and Heteromyidae) or sciuromorph and caviomorph rodents.
By Northern-hybridization, 4.5SI RNA has been detected in the common rat (R. norvegicus, Muridae), golden hamster (Mesocricetus auratus, Cricetidae), and Russian mole rat (Spalax microphthalmus, Spalacidae), but not in the related great jerboa (Allactaga jaculus, Dipodidae) or in four non-myomorph rodent species tested. cDNA derived from 4.5SI RNA of M. auratus and S. microphthalmus has been cloned and sequenced. The hamster RNA is found to differ from rat 4.5SI RNA by only one nucleotide substitution. For the mole rat, two variants of 4.5SI RNA are detected: short (S) and long (L) with length 101 and 108 nt, respectively. The L variant differs from the S variant
as well as from murid and cricetid 4.5SI RNAs by both a 7 nt insertion and a varying number of nucleotide substitutions. The sequence similarity between the spalacid
S-variant and murid/crecitid variants of 4.5SI RNA is 90%. Judging from species distribution, 4.5SI RNA genes emerged during the same period of time as the related short interspersed element B2 arose. This occurred after
the divergence of Dipodidae lineage but before the branching of Spalicidae/Rhizomyidae lineage from a common myomorph rodent
stem. S variant genes seemed to emerge in a common ancestor of spalacids and rhizomyds whereas L variant genes formed in spalacids
following the divergence of these two families. The low rate of evolutionary changes of 4.5SI RNA, at least, in murids and cricetids (6 × 10−4 substitutions per site per million years), suggests that this RNA is under selection constraint and have a function. This
is a remarkable fact if the recent origin and narrow species distribution range of 4.5SI RNA genes is taken into account. Genes with narrow species distribution are proposed to be referred to as stenogenes.
Received: 11 December 2000 / Accepted: 27 August 2001 相似文献
14.
A DNA fragment containing short tandem repeat sequences (approximately 86-bp repeat) was isolated from a Xenopus laevis cDNA library. Southern blot and in situ hybridization analyses revealed that the repeat was highly dispersed in the genome and was present at approximately 1 million
copies per haploid genome. We named this element Xstir (Xenopus short tandemly and invertedly repeating element) after its arrangement in the genome. The majority of the genomic Xstir sequences
were digested to monomer and dimer sizes with several restriction enzymes. Their sequences were found to be highly homogeneous
and organized into tandem arrays in the genome. Alignment analyses of several known sequences showed that some of the Xstir-like
sequences were also organized into interspersed inverted repeats. The inverted repeats consisted of an inverted pair of two
differently modified Xstirs separated by a short insert. In addition, these were framed by another novel inverted repeat (Xstir-TIR).
The Xstir-TIR sequence was also found at the ends of tandem Xstir arrays. Furthermore, we found that Xstir-TIR was linked
to a motif characterizing the T2 family which belonged to a vertebrate MITE (miniature inverted-repeat transposable element)
family, suggesting the importance of Xstir-TIR for their amplification and transposition. The present study of 11 anuran and
2 urodele species revealed that Xstir or Xstir-like sequences were extensively amplified in the three Xenopus species. Genomic Xstir populations of X. borealis and X. laevis were mutually indistinguishable but significantly different from that of X. tropicalis.
Received: 5 April 2000 / Accepted: 3 August 2000 相似文献
15.
Telomeres of most insects are composed of simple (TTAGG)
n
repeats that are synthesized by telomerase. However, in some dipteran insects such as Drosophila melanogaster, (TTAGG)
n
repeats or telomerase activity has not been detected. Although telomere structure is well documented in Diptera and Lepidoptera,
very limited information is available on lower insect groups. To understand general aspects of telomere function and evolution
in insects, we endeavored to characterize structures of the telomeric and subtelomeric regions in a lower insect, the Taiwan
cricket, Teleogryllus taiwanemma. FISH analysis of this insect's chromosomes demonstrated (TTAGG)
n
repeat elements in all distal ends. Just proximal to the telomeric repeats, the highly conserved 9-kb long terminal unit
(LTU) sequences are tandemly repeated. These were observed in four of six chromosomes, three autosomal ends, and one X-chromosomal
end. LTU sequences represent about 0.2% of the T. taiwanemma genome. Each LTU contains a core (TTAGG)8-like sequence (TRLS) and five types of conserved sequences—ST (short telomere associated), J (joint), X, SR (satellite sequence
rich), and Y—which vary in length from about 150 bp to 2.7 kb. The LTU sequence is defined as ST–J–TRLS–SR–X–Y–X–Y–X. Most
LTU regions may be derived from the ancestral common sequence, which is observed in ST regions six times and at many other
LTU sites. We could not find the LTU-like sequence in three other crickets including the closest species, T. emma, suggesting that the LTU in T. taiwanemma has been rapidly amplified in subtelomeric regions through recent evolutional events. It is also suggested that the highly
conserved structure of the LTU is maintained by recombination and may contribute to telomere elongation, as seen in dipteran
insects.
Received: 6 August 2001/Accepted: 10 October 2001 相似文献
16.
Frédérique Viard Pierre Franck Marie-Pierre Dubois Arnaud Estoup Philippe Jarne 《Journal of molecular evolution》1998,47(1):42-51
Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base
pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee
Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount
of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and
one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing
effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the
molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning
that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F
st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions.
Received: 21 July 1997 / Accepted: 29 January 1998 相似文献
17.
Southern hybridization data suggest that the male sex-determining locus, Sry, is often duplicated in rodents. Here we explore DNA sequence evolution of orthologous and paralogous copies of Sry isolated from six species of African murines. PCR amplification followed by direct sequencing revealed from two to four copies
of Sry per species. All copies include a long open reading frame, with a stop codon that coincides closely with the stop codon of
the house mouse, Mus musculus, a species known to have a single copy of Sry. A phylogenetic analysis suggests that there are at least seven paralogous copies of Sry in this group of rodents. Putative orthologues are identical; sequence divergence among putative paralogues ranges from 1
to 8% (excluding the CAG repeat), with much lower levels of divergence in the high-mobility group (HMG-box) region than in
the C-terminal region. A high proportion of nucleotide substitutions in both regions result in amino-acid replacement. The
long open reading frame, conserved HMG-box, and pattern of evolution of the putative paralogues suggest that they are functional.
Received: 4 October 1996 / Accepted: 17 January 1997 相似文献
18.
E. Rosato A. A. Peixoto A. Gallippi C. P. Kyriacou R. Costa 《Journal of molecular evolution》1996,42(4):392-408
The D. melanogaster clock gene period (per) is an internally repetitive gene encoding a tandem array of Thr-Gly codons that are highly polymorphic in length in European
natural populations. The two major length variants, (Thr-Gly)20 and (Thr-Gly)17, show a highly significant latitudinal cline. In this study we present the complete sequence of the Thr-Gly region of 91
individuals from 6 natural populations of D. melanogaster, 5 from Europe and 1 from North Africa. We further characterized these 91 individuals for polymorphic sites in two other regions,
one upstream and one downstream of the Thr-Gly repeat. We used the haplotypic combinations of Thr-Gly allele with flanking
markers in an attempt to identify the mechanisms involved in the evolution of the D. melanogaster Thr-Gly region and to infer the phylogenetic relationship existing among the Thr-Gly alleles. We observe evidence for both
intra- and interallelic mutational mechanisms, including replication slippage, unequal crossing-over, and gene conversion.
Received: 22 August 1995 / Accepted: 17 October 1995 相似文献
19.
Satellite DNA profiles have been characterized in the congeneric species
Palorus ratzeburgii, Palorus subdepressus, Palorus genalis, and Palorus
ficicola (Coleoptera, Insecta), each of which contains a single, A + T-rich
satellite DNA comprising a considerable portion of the genome (20%-40%).
These satellites exhibit insignificant mutual sequence similarity. Using
PCR assay, it has been shown that all four sequences are present in each of
the tested Palorus species: one of them is amplified into a high copy
number or a major satellite, while the three others are in the form of
low-copy-number repeats estimated to make up approximately 0.05% of the
genome. Each of the four satellites is interspecifically high conserved
concerning the sequence, monomer length, and tandem repeat organization.
Major, as well as low- copy-number, satellites are colocalized in the
regions of pericentromeric heterochromatin on all chromosomes of the
complement. The low-copy-number satellites are dispersed between the large
arrays of the major satellite over the whole heterochromatic block. Our
results explain satellite DNA evolution, confirming the hypothesis that
related species share a "library" of conserved satellite sequences, some of
which could be amplified into a major satellite. Due to the evolutionary
dynamics of satellite DNAs, the content of the "library" is variable; the
elimination of some sequences parallels the creation of the new ones.
Quantitative changes in satellite DNAs, induced by occasional amplification
of satellite repeat from the "library", could possibly occur in the course
of the speciation process, thus forming a species-specific profile of
satellite DNAs.
相似文献
20.
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