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1.
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
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.
Miroslav Plohl Nevenka Mestrović Branka Bruvo Đurđica Ugarković 《Journal of molecular evolution》1998,46(2):234-239
A novel highly abundant satellite DNA comprising 20% of the genome has been characterized in Palorus subdepressus (Insecta, Coleoptera). The 72-bp-long monomer sequence is composed of two copies of T2A5T octanucleotide alternating with 22-nucleotide-long elements of an inverted repeat. Phylogenetic analysis revealed clustering
of monomer sequence variants into two clades. Two types of variants are prevalently organized in an alternating pattern, thus
showing a tendency to generate a new complex repeating unit 144 bp in length. Fluorescent in situ hybridization revealed even
distribution of the satellite in the region of pericentric heterochromatin of all 20 chromosomes. P. subdepressus satellite sequence is clearly species specific, lacking similarity even with the satellite from congeneric species P. ratzeburgii. However, on the basis of similarity in predicted tertiary structure induced by intrinsic DNA curvature and in repeat length,
P. subdepressus satellite can be classified into the same group with satellites from related tenebrionid species P. ratzeburgii, Tenebrio molitor, and T. obscurus. It can be reasonably inferred that repetitive sequences of different origin evolve under constraints to adopt and conserve
particular features. Obtained results suggest that the higher-order structure and repeat length, but not the nucleotide sequence
itself, are maintained through evolution of these species.
Received: 23 April 1997 / Accepted: 11 July 1997 相似文献
5.
The subspecies Chironomus thummi thummi and C. t. piger display dramatic differences in the copy number and chromosomal localization of a tandemly repeated DNA family (Cla elements).
In order to analyze the evolutionary dynamics of this repeat family, we studied the organization of Cla elements in the related
outgroup species C. luridus. We find three different patterns of Cla element organization in C. luridus, showing that Cla elements may be either strictly tandem-repetitive or be an integral part of two higher-order tandem repeats
(i.e., Hinf[lur] elements, Sal[lur] elements). All three types of Cla-related repeats are localized in the centromeres of C. luridus chromosomes. This suggests that the dispersed chromosomal localization of Cla elements in C. t. thummi may be the result of an amplification and transposition during evolution of this subspecies.
Received: 22 May 1996 / Accepted: 8 October 1996 相似文献
6.
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
7.
A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled
to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general
pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids
from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The
cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic
distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined
as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts.
Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these
high evolutionary rates were significantly higher among geophagine cichlids.
Received: 18 September 1998 / Accepted: 16 December 1998 相似文献
8.
Dorota Szczepanik Paweł Mackiewicz Maria Kowalczuk Agnieszka Gierlik Aleksandra Nowicka Mirosław R. Dudek Stanisław Cebrat 《Journal of molecular evolution》2001,52(5):426-433
One of the main causes of bacterial chromosome asymmetry is replication-associated mutational pressure. Different rates of
nucleotide substitution accumulation on leading and lagging strands implicate qualitative and quantitative differences in
the accumulation of mutations in protein coding sequences lying on different DNA strands. We show that the divergence rate
of orthologs situated on leading strands is lower than the divergence rate of those situated on lagging strands. The ratio
of the mutation accumulation rate for sequences lying on lagging strands to that of sequences lying on leading strands is
rather stable and time-independent. The divergence rate of sequences which changed their positions, with respect to the direction
of replication fork movement, is not stable—sequences which have recently changed their positions are the most prone to mutation
accumulation. This effect may influence estimations of evolutionary distances between species and the topology of phylogenetic
trees.
Received: 24 July 2000 / Accepted: 16 January 2001 相似文献
9.
10.
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
11.
In eight hagfish species, it is known that chromosome elimination occurs during early embryogenesis, and some highly repetitive
DNA families, restricted to germ cells, have been isolated. One of these families, ``EEEo2,' has been isolated as DNA fragments
by restriction enzyme analyses from Eptatretus okinoseanus and E. cirrhatus. In this study, EEEo2 sequences were isolated from germline DNA in E. burgeri, Paramyxine sheni, and P. atami using PCR methods. Sequence analysis revealed that these sequences are intraspecifically homogeneous, except in E. burgeri, and are interspecifically conserved with heterogeneity. The intraspecific sequence variability tends to decrease as the copy
number increases. These results indicate that EEEo2 has evolved in a concerted manner. Moreover, an ancestral repeating motif
consisting of triplicate subrepeats was deduced. These results suggest that EEEo2 arose as an initial amplification of this
subrepeat and has evolved by saltatory replication. Phylogenetic analyses suggested the possibility that EEEo2 in E. okinoseanus and E. cirrhatus has been subjected to strong homogenizing forces for concerted evolution, whereas the force is weak in E. burgeri. In addition, EEEo2 in P. sheni and P. atami appear to have been incompletely subjected to these forces. Chromosomal in situ hybridization experiments revealed that EEEo2
sequences were located along almost their entire length of several heterochromatic chromosomes that are restricted to germ
cells. These chromosomes are disposed to form a secondary association during the first meiotic metaphases, except in P. sheni. This chromosomal distribution may promote a concerted mode of sequence evolution in both nonhomologous chromosomes and homologous
chromosomes and reflect the differential driving forces between species.
Received: 17 April 1999 / Accepted: 10 September 1999 相似文献
12.
Weinreich DM 《Journal of molecular evolution》2001,52(1):40-50
A higher rate of molecular evolution in rodents than in primates at synonymous sites and, to a lesser extent, at amino acid
replacement sites has been reported previously for most nuclear genes examined. Thus in these genes the average ratio of amino
acid replacement to synonymous substitution rates in rodents is lower than in primates, an observation at odds with the neutral
model of molecular evolution. Under Ohta's mildly deleterious model of molecular evolution, these observations are seen as
the consequence of the combined effects of a shorter generation time (driving a higher mutation rate) and a larger effective
population size (resulting in more effective selection against mildly deleterious mutations) in rodents. The present study
reports the results of a maximum-likelihood analysis of the ratio of amino acid replacements to synonymous substitutions for
genes encoded in mitochondrial DNA (mtDNA) in these two lineages. A similar pattern is observed: in rodents this ratio is
significantly lower than in primates, again consistent only with the mildly deleterious model. Interestingly the lineage-specific
difference is much more pronounced in mtDNA-encoded than in nuclear-encoded proteins, an observation which is shown to run
counter to expectation under Ohta's model. Finally, accepting certain fossil divergence dates, the lineage-specific difference
in amino acid replacement-to-synonymous substitution ratio in mtDNA can be partitioned and is found to be entirely the consequence
of a higher mutation rate in rodents. This conclusion is consistent with a replication-dependent model of mutation in mtDNA.
Received: 24 September 1999 / Accepted: 18 September 2000 相似文献
13.
Albert Jeltsch 《Journal of molecular evolution》1999,49(1):161-164
Circular permutations of genes during molecular evolution often are regarded as elusive, although a simple model can explain
these rearrangements. The model assumes that first a gene duplication of the precursor gene occurs in such a way that both
genes become fused in frame, leading to a tandem protein. After generation of a new start codon within the 5′ part of the
tandem gene and a stop at an equivalent position in the 3′ part of the gene, a protein is encoded that represents a perfect
circular permutation of the precursor gene product. The model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases. β- and γ-type enzymes of this family can be interconverted by a single circular permutation event.
Interestingly, tandem proteins, proposed as evolutionary intermediates during circular permutation, can be directly observed
in the case of adenine methyltransferases, because some enzymes belonging to type IIS, like the FokI methyltransferase, are built up by two fused enzymes, both of which are active independently of each other. The mechanism
for circular permutation illustrated here is very easy and applicable to every protein. Thus, circular permutation can be
regarded as a normal process in molecular evolution and a changed order of conserved amino acid motifs should not be interpreted
to argue against divergent evolution.
Received: 17 November 1998 / Accepted: 19 February 1999 相似文献
14.
Characterization and Evolution of the Mitochondrial DNA Control Region in Hornbills (Bucerotiformes)
We determined the mitochondrial DNA control region sequences of six Bucerotiformes. Hornbills have the typical avian gene
order and their control region is similar to other avian control regions in that it is partitioned into three domains: two
variable domains that flank a central conserved domain. Two characteristics of the hornbill control region sequence differ
from that of other birds. First, domain I is AT rich as opposed to AC rich, and second, the control region is approximately
500 bp longer than that of other birds. Both these deviations from typical avian control region sequence are explainable on
the basis of repeat motifs in domain I of the hornbill control region. The repeat motifs probably originated from a duplication
of CSB-1 as has been determined in chicken, quail, and snowgoose. Furthermore, the hornbill repeat motifs probably arose before
the divergence of hornbills from each other but after the divergence of hornbills from other avian taxa. The mitochondrial
control region of hornbills is suitable for both phylogenetic and population studies, with domains I and II probably more
suited to population and phylogenetic analyses, respectively. 相似文献
15.
A long repetitive DNA sequence (OtY8) has been cloned from male chinook salmon and its genomic organization has been characterized.
The repeat has a unit length of 8 kb and is present approximately 300 times per diploid male nucleus. All internal fragments
within the 8-kb repeat segregate from father to son, suggesting that the entire repeat unit is located on the Y chromosome.
The organization of this sequence into an 8-kb repeat unit is restricted to the Y chromosome, as are several male-specific
repeat subtypes identified on the basis of restriction-site variation. The repeat possesses only weak internal sequence similarities,
suggesting that OtY8 has not arisen by duplication of a smaller repeat unit, as is the case for other long tandem arrays found
in eukaryotes. Based on a laddered pattern arising from partial digestion of genomic DNA with a restriction enzyme which cuts
only once per repeat unit, this sequence is not dispersed on the Y chromosome but is organized as a head-to-tail tandem array.
Pulse-gel electrophoresis reveals that the direct-tandem repeats are organized into at least six separate clusters containing
approximately 12 to 250 copies, comprising some 2.4 Mb of Y-chromosomal DNA in total. Related sequences with nucleotide substitutions
and DNA insertions relative to the Y-chromosomal fragment are found elsewhere in the genome but at much lower copy number
and, although similar sequences are also found in other salmonid species, the amplification of the repeat into a Y-chromosome-linked
tandem array is only observed in chinook salmon. The OtY8 repetitive sequence is genetically tightly associated with the sex-determination
locus and provides an opportunity to examine the evolution of the Y chromosome and sex determination process in a lower vertebrate.
Received: 4 April 1997 / Accepted: 22 July 1997 相似文献
16.
Alexey N. Fedorov Larisa V. Fedorova Vernata V. Grechko Dmitrii M. Ryabinin Valentina A. Sheremet'eva Anna A. Bannikova Alexei A. Lomov Alexei P. Ryskov Ilya S. Darevsky 《Journal of molecular evolution》1999,48(1):69-76
A specially optimized restriction analysis of highly repetitive DNA elements, called DNA taxonprint, was applied for phylogenetic
study of primates and lizards. It was shown that electrophoretic bands of DNA repeats revealed by the taxonprint technique
have valuable properties for molecular systematics. Approximately half of taxonprint bands (TB) are invariable and do not
disappear from the genomes during evolution or change spontaneously. Presumably these invariable bands are restriction fragments
of dispersed DNA repeats. Another group represents variable taxonprint bands that differ even between closely related species.
These variable bands are probably represented by tandem DNA repeats and could be used as species-specific markers. It was
shown that taxonprint bands are independent characters since the appearance of a new taxonprint band does not change the previous
band pattern. Phylogenetic reconstruction carried out on taxonprint data demonstrated that this approach could be of general
utility for molecular systematics and species identification.
Received: 12 January 1998 / Accepted: 16 May 1998 相似文献
17.
Takehiro Kusakabe Isato Araki Noriyuki Satoh William R. Jeffery 《Journal of molecular evolution》1997,44(3):289-298
The origin and evolutionary relationship of actin isoforms was investigated in chordates by isolating and characterizing
two new ascidian cytoplasmic and muscle actin genes. The exon–intron organization and sequences of these genes were compared
with those of other invertebrate and vertebrate actin genes. The gene HrCA1 encodes a cytoplasmic (nonmuscle)-type actin, whereas the MocuMA2 gene encodes an adult muscle-type actin. Our analysis of these genes showed that intron positions are conserved among the
deuterostome actin genes. This suggests that actin gene families evolved from a single actin gene in the ancestral deuterostome.
Sequence comparisons and molecular phylogenetic analyses also suggested a close relationship between the ascidian and vertebrate
actin isoforms. It was also found that there are two distinct lineages of muscle actin isoforms in ascidians: the larval muscle
and adult body-wall isoforms. The four muscle isoforms in vertebrates show a closer relationship to each other than to the
ascidian muscle isoforms. Similarly, the two cytoplasmic isoforms in vertebrates show a closer relationship to each other
than to the ascidian and echinoderm cytoplasmic isoforms. In contrast, the two types of ascidian muscle actin diverge from
each other. The close relationship between the ascidian larval muscle actin and the vertebrate muscle isoforms was supported
by both neighbor-joining and maximum parsimony analyses. These results suggest that the chordate ancestor had at least two
muscle actin isoforms and that the vertebrate actin isoforms evolved after the separation of the vertebrates and urochordates.
Received: 20 June 1996 / Accepted: 16 October 1996 相似文献
18.
M. Mar Albà Mauro F. Santibáñez-Koref John M. Hancock 《Journal of molecular evolution》2001,52(3):249-259
Polyglutamine repeats within proteins are common in eukaryotes and are associated with neurological diseases in humans. Many
are encoded by tandem repeats of the codon CAG that are likely to mutate primarily by replication slippage. However, a recent
study in the yeast Saccharomyces cerevisiae has indicated that many others are encoded by mixtures of CAG and CAA which are less likely to undergo slippage. Here we
attempt to estimate the proportions of polyglutamine repeats encoded by slippage-prone structures in species currently the
subject of genome sequencing projects. We find a general excess over random expectation of polyglutamine repeats encoded by
tandem repeats of codons. We nevertheless find many repeats encoded by nontandem codon structures. Mammals and Drosophila display extreme opposite patterns. Drosophila contains many proteins with polyglutamine tracts but these are generally encoded by interrupted structures. These structures
may have been selected to be resistant to slippage. In contrast, mammals (humans and mice) have a high proportion of proteins
in which repeats are encoded by tandem codon structures. In humans, these include most of the triplet expansion disease genes.
Received: 17 August 2000 / Accepted: 20 November 2000 相似文献
19.
A phylogenetic analysis of the five major families of DNA polymerase is presented. Viral and plasmid sequences are included
in this compilation along with cellular enzymes. The classification by Ito and Braithwaite (Ito and Braithwaite 1991) of the
A, B, C, D, and X families has been extended to accommodate the ``Y family' of DNA polymerases that are related to the eukaryotic
RAD30 and the bacterial UmuC gene products. After analysis, our data suggest that no DNA polymerase family was universally
conserved among the three biological domains and no simple evolutionary scenario could explain that observation. Furthermore,
viruses and plasmids carry a remarkably diverse set of DNA polymerase genes, suggesting that lateral gene transfer is frequent
and includes non-orthologous gene displacements between cells and viruses. The relationships between viral and host genes
appear very complex. We propose that the gamma DNA polymerase of the mitochondrion replication apparatus is of phage origin
and that this gene replaced the one in the bacterial ancestor. Often there was no obvious relation between the viral and the
host DNA polymerase, but an interesting exception concerned the family B enzymes: in which ancient gene exchange can be detected
between the viruses and their hosts. Additional evidence for horizontal gene transfers between cells and viruses comes from
an analysis of the small damage-inducible DNA polymerases. Taken together, these findings suggest a complex evolutionary history
of the DNA replication apparatus that involved significant exchanges between viruses, plasmids, and their hosts. 相似文献
20.
Jih-Shiou Liu Yau-Heiu Hsu Tzu-Yu Huang Na-Sheng Lin 《Journal of molecular evolution》1997,44(2):207-213
Satellite RNA of bamboo mosaic potexvirus (satBaMV) is a linear RNA molecule which encodes a 20-kDa nonstructural protein.
Sequences of seven different satBaMV isolates from bamboo hosts in three genera showed 0.7% to 7.5% base variation which spanned
the whole RNA molecule. However, the putative 20-kDa open reading frame was all preserved in these isolates. The phylogenetic
relationship based on the nucleotide sequence did not show particular grouping of satBaMV from the host in one genus; neither
was the grouping of satBaMV evident by location of sampling. Putative secondary structures of the 3′ untranslated regions
showed a basic pattern with conserved hexanucleotides (ACCUAA) and polyadenylation signal (AAUAAA) located in the loop regions.
Although the satBaMV-encoded 20-kDa protein is a nonstructural protein, its predicted secondary structure contains eight-stranded
β-sheets which may form ``jelly-roll' structure similar to that found in capsid protein encoded by satellite virus of panicum
mosaic virus.
Received: 26 June 1996 / Accepted: 9 September 1996 相似文献