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1.
Characterization of Repetitive DNA Elements in Arabidopsis 总被引:1,自引:0,他引:1
We have applied computational methods to the available database and identified several families of repetitive DNA elements
in the Arabidopsis thaliana genome. While some of the elements have features expected of either miniature inverted-repeat transposable elements (MITEs)
or retrotransposons, the most abundant class of repetitive elements, the AthE1 family, is structurally related to neither. The AthE1 family members are defined by conserved 5′ and 3′ sequences, but these terminal sequences do not represent either inverted
or direct repeats. AthE1 family members with greater than 98% identity are easily identified on different Arabidopsis chromosomes. Similar to nonautonomous DNA-based transposon families, the AthE1 family contains members in which the conserved terminal domains flank unrelated sequences. The primary utility of characterizing
repetitive sequences is in defining, at least in part, the evolutionary architecture of specific Arabidopsis loci. The repetitive elements described here make up approximately 1% of the available Arabidopsis thaliana genomic sequence.
Received: 13 October 1998 / Accepted: 30 December 1998 相似文献
2.
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
3.
We compared deleted copies of the seven mauritiana subfamilies of mariner transposable elements in species of the Drosophilidae. All elements were detected by PCR using the inverted terminal repeats
of the Mos1 element of Drosophila mauritiana as primers. A higher frequency of breakpoints in the 5′ part of the element compared to the 3′ part was observed. Of the
27 deletions, 9 (33%) occurred between short direct repeats (SDR) of 5 to 8 bp. The SDRs can be at or close to the breakpoints
of the deletion. A deleted copy of D. simulans (St. Martin population) had three repeats of a motif present only once in the complete consensus sequence. The high frequency
of SDRs at or near the breakpoints of the deletions strongly suggests that some of them do not occur at random. Mechanisms
that might explain these deletions, such as unequal crossing-over, ectopic recombination, and abortive gap repair, are discussed.
Received: 22 December 2000 / Accepted: 12 July 2001 相似文献
4.
Identification of transposon-like elements in non-coding regions of tomato ACC oxidase genes 总被引:4,自引:0,他引:4
B. Blume C. S. Barry A. J. Hamilton M. Bouzayen D. Grierson 《Molecular & general genetics : MGG》1997,254(3):297-303
1-aminocyclopropane-1-carboxylate (ACC) oxidase, which catalyses the terminal step in ethylene biosynthesis, is encoded by
a small multigene family in tomato that is differentially expressed in response to developmental and environmental cues. In
this study we report the isolation and sequencing of approximately 2 kb of 5′-flanking sequence of three tomato ACC oxidase
genes (LEACO1, LEACO2, LEACO3) and the occurrence of class I and class II mobile element-like insertions in promoter and intron regions of two of them.
The LEACO1 upstream region contains a 420-bp direct repeat which is present in multiple copies in the tomato genome and is very similar
to sequences in the promoters of the tomato E4 and 2A11 genes. The region covering the repeats resembles the remnant of a retrotransposon. Two copies of a small transposable element,
belonging to the Stowaway inverted repeat element family, have been found in the 5′-flanking sequence and the third intron of LEACO3.
Received: 8 August 1996 / Accepted: 4 November 1996 相似文献
5.
Tandemly repeated sequences are a major component of the eukaryotic genome. Although the general characteristics of tandem
repeats have been well documented, the processes involved in their origin and maintenance remain unknown. In this study, a
region on the paternal sex ratio (PSR) chromosome was analyzed to investigate the mechanisms of tandem repeat evolution. The
region contains a junction between a tandem array of PSR2 repeats and a copy of the retrotransposon NATE, with other dispersed repeats (putative mobile elements) on the other side of the element. Little similarity was detected
between the sequence of PSR2 and the region of NATE flanking the array, indicating that the PSR2 repeat did not originate from the underlying NATE sequence. However, a short region of sequence similarity (11/15 bp) and an inverted region of sequence identity (8 bp) are
present on either side of the junction. These short sequences may have facilitated nonhomologous recombination between NATE and PSR2, resulting in the formation of the junction. Adjacent to the junction, the three most terminal repeats in the PSR2
array exhibited a higher sequence divergence relative to internal repeats, which is consistent with a theoretical prediction
of the unequal exchange model for tandem repeat evolution. Other NATE insertion sites were characterized which show proximity to both tandem repeats and complex DNAs containing additional dispersed
repeats. An ``accretion model' is proposed to account for this association by the accumulation of mobile elements at the
ends of tandem arrays and into ``islands' within arrays. Mobile elements inserting into arrays will tend to migrate into
islands and to array ends, due to the turnover in the number of intervening repeats.
Received: 18 August 1997 / Accepted: 18 September 1998 相似文献
6.
Atsushi Hoshino Yoshishige Inagaki Shigeru Iida 《Molecular genetics and genomics : MGG》1995,247(1):114-117
The 6.4 kb transposable element Tpn1 belonging to the En/Spm family was found within one of the DFR (dihydroflavonol-4-reductase) genes for anthocyanin biosynthesis in a line of Japanese morning glory (Pharbitis nil) bearing variegated flowers. Sequencing of the Tpn1 element revealed that it is 6412 by long and carries 28-bp perfect terminal inverted repeats. Its subterminal repetitive regions, believed to be the cis-acting sequences for transposition, show striking structural features. Twenty-two copies of the 10-bp sequence motif GACAACGGTT can be found as direct or inverted repeats within 650 by of the 5′ end of the element, and 33 copies of the sequence motif lie within 800 by of the 3′ terminus. All these 22 copies of the sequence motif near the 5′ terminus and 30 copies in the 3′ terminal region are arranged as inverted repeats and 3–8 by AT-rich sequences are detected between these inverted repeats. In addition, four copies of 122-bp tandem repeats and six copies of 104-bp tandem repeats are present in the 5′ and 3′ subterminal repetitive regions, respectively. No large open reading frame characteristic of autonomous elements of the En/Spm family can be detected within the element. The results are discussed with respect to heritable changes in flower variegation in this line of Japanese morning glory. 相似文献
7.
Johannes A. Jehle Antje Nickel Just M. Vlak Horst Backhaus 《Journal of molecular evolution》1998,46(2):215-224
We characterized an insertion mutant of the baculovirus Cydia pomonella granulovirus (CpGV), which contained a transposable element of 3.2 kb. This transposon, termed TCp3.2, has unusually long
inverted terminal repeats (ITRs) of 756 bp and encodes a defective gene for a putative transposase. Amino acid sequence comparison
of the defective transposase gene revealed a distant relationship to a putative transposon in Caenorhabditis elegans which also shares some similarity of the ITRs. Maximum parsimony analysis of the predicted amino acid sequences of Tc1- and
mariner-like transposases available from the GenBank data base grouped TCp3.2 within the superfamily of Tc1-like transposons.
DNA hybridization indicated that TCp3.2 originated from the genome of Cydia pomonella, which is the natural host of CpGV, and is present in less than 10 copies in the C. pomonella genome. The transposon TCp3.2 most likely was inserted into the viral genome during infection of host larvae. TCp3.2 and
the recently characterized Tc1-like transposon TC14.7 (Jehle et al. 1995), which was also found in a CpGV mutant, represent
a new family of transposons found in baculovirus genomes. The occasional horizontal escape of different types of host transposons
into baculovirus genomes evokes the question about the possible role of baculoviruses as an interspecies vector in the horizontal
transmission of insect transposons.
Received: 27 February 1997 / Accepted: 16 May 1997 相似文献
8.
9.
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
10.
Atsushi Hoshino Yoshishige Inagaki Shigeru Iida 《Molecular & general genetics : MGG》1995,247(1):114-117
The 6.4 kb transposable element Tpn1 belonging to the En/Spm family was found within one of the DFR (dihydroflavonol-4-reductase) genes for anthocyanin biosynthesis in a line of Japanese morning glory (Pharbitis nil) bearing variegated flowers. Sequencing of the Tpn1 element revealed that it is 6412 by long and carries 28-bp perfect terminal inverted repeats. Its subterminal repetitive regions, believed to be the cis-acting sequences for transposition, show striking structural features. Twenty-two copies of the 10-bp sequence motif GACAACGGTT can be found as direct or inverted repeats within 650 by of the 5 end of the element, and 33 copies of the sequence motif lie within 800 by of the 3 terminus. All these 22 copies of the sequence motif near the 5 terminus and 30 copies in the 3 terminal region are arranged as inverted repeats and 3–8 by AT-rich sequences are detected between these inverted repeats. In addition, four copies of 122-bp tandem repeats and six copies of 104-bp tandem repeats are present in the 5 and 3 subterminal repetitive regions, respectively. No large open reading frame characteristic of autonomous elements of the En/Spm family can be detected within the element. The results are discussed with respect to heritable changes in flower variegation in this line of Japanese morning glory. 相似文献
11.
Annexin homologues in the kingdoms of Planta and Protista were characterized by molecular sequence analysis to determine
their phylogenetic and structural relationship with annexins of Animalia. Sequence fragments from 19 plant annexins were identified
in sequence databases and composite sequences were also assembled from expressed sequence tags for Arabidopsis thaliana. Length differences in protein amino-termini and evidence for unique exon splice sites indicated that plant annexins were
distinct from those of animals. A third annexin gene of Giardia lamblia (Anx21-Gla) was identified as a distant relative to other protist annexins and to those of higher eukaryotes, thus providing a suitable
outgroup for evolutionary reconstruction of the family tree. Rooted evolutionary trees portrayed protist, plant, and Dictyostelium annexins as early, monophyletic ramifications prior to the appearance of closely related animal annexin XIII. Molecular phylogenetic
analyses of DNA and protein sequence alignments revealed at least seven separate plant subfamilies, represented by Anx18 (alfalfa, previously classified), Anx22 (thale cress), Anx23 (thale cress, cotton, rape and cabbage), Anx24 (bell pepper and tomato p34), Anx25 (strawberry, horseradish, pea, soybean, and castor bean), Anx26-Zma, and Anx27-Zma (maize). Other unique subfamilies may exist for rice, tomato p35, apple, and celery annexins. Consensus sequences compiled
for each eukaryotic kingdom showed some breakdown of the ``annexin-fold' motif in repeats 2 and 3 of protist and plant annexins
and a conserved codon deletion in repeat 3 of plants. The characterization of distinct annexin genes in plants and protists
reflects their comparable diversity among animal species and offers alternative models for the comparative study of structure–function
relationships within this important gene family.
Received: 30 May 1996 / Accepted: 20 August 1996 相似文献
12.
For the first time, mariner elements were found in insect parasitic nematodes. Full-length elements were isolated from the rhabditid Heterorhabditis bacteriophora. They were 1279 bp long, flanked by two 30-bp inverted repeats, and were able to encode a putative 358-amino acid transposase.
These elements were present in about 30 copies in the H. bacteriophora genome, but their distribution among closely related Heterorhabditis and Steinernema genera was patchy. DNA and encoded peptide sequences of H. bacteriophora mariners showed greater similarity to the mariner of the coleopteran Carpelimus sp. than to the mariners of the rhabditid Caenorhabditis elegans. The possibility of horizontal transfer was investigated by examination of a host for Heterorhabditis nematodes, a beetle of the Phyllophaga sp. Mariner elements were found in this insect, but they were not very similar to the H. bacteriophora elements. Finally, the H. bacteriophora mariners formed a group with those of invertebrates, suggesting vertical transmission from a common ancestor.
Received: 14 November 1997 / Accepted: 4 August 1998 相似文献
13.
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
14.
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
15.
M. E. Manetti M. Rossi M. Nakabashi M. A. Grandbastien Marie Anne Van Sluys 《Molecular genetics and genomics : MGG》2009,281(3):261-271
Eukaryotic genome expansion/retraction caused by LTR-retrotransposon activity is dependent on the expression of full length
copies to trigger efficient transposition and recombination-driven events. The Tnt1 family of retrotransposons has served
as a model to evaluate the diversity among closely related elements within Solanaceae species and found that members of the
family vary mainly in their U3 region of the long terminal repeats (LTRs). Recovery of a full length genomic copy of Retrosol
was performed through a PCR-based approach from wild potato, Solanum oplocense. Further characterization focusing on both LTR sequences of the amplified copy allowed estimating an approximate insertion
time at 2 million years ago thus supporting the occurrence of transposition cycles after genus divergence. Copy number of
Tnt1-like elements in Solanum species were determined through genomic quantitative PCR whereby results sustain that Retrosol in Solanum species is a low copy number retrotransposon (1–4 copies) while Retrolyc1 has an intermediate copy number (38 copies) in
S. peruvianum. Comparative analysis of retrotransposon content revealed no correlation between genome size or ploidy level and Retrosol
copy number. The tetraploid cultivated potato with a cellular genome size of 1,715 Mbp harbours similar copy number per monoploid
genome than other diploid Solanum species (613–884 Mbp). Conversely, S. peruvianum genome (1,125 Mbp) has a higher copy number. These results point towards a lineage specific dynamic flux regarding the history
of amplification/activity of Tnt1-like elements in the genome of Solanum species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Cab-1 is a complex genetic locus in tomato consisting of four clustered genes encoding chlorophyll a/b-binding polypeptide. Southern blot analysis of total tomato DNA with genomic clones corresponding to the Cab-1 locus has revealed the presence of a repetitive element in the 3 kb spacer regions between two of these genes. This repetitive element, named CR1, has been characterized via sequencing, genetic mapping and hybridization to related solanaceous species. Results indicate that there are as many as 30 copies of this element in the tomato genome and that most, if not all, are found at independent loci. Sites corresponding to 12 of the repeats have been located on different regions of chromosomes 2, 4, 5, 7, 10 and 11. A 1.6 kb PstI-EcoRI fragment from the Cab-1 locus containing the element was sequenced and found to be 75% AT-rich. No open reading frames larger than 150 bp were detected. Several imperfect inverted repeats flanked by direct repeats could be found at the ends of the element. This arrangement is reminiscent of known transposons. Southern hybridization analysis indicates that multiple copies of CR1 exist in all species of the genus Lycopersicon as well as in Solanum lycopersicoides and S. tuberosum (potato), but not in eggplant, pepper, petunia, Datura or tobacco. Melt-off experiments indicate that members of the CR1 family in the tomato genome are more closely related to one another than to homologous members in the genomes of S. lycopersicoides or S. tuberosum, suggesting some type of concerted evolution. 相似文献
17.
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
18.
Three loci in the genome of the white-footed mouse, Peromyscus leucopus, were examined for the presence or absence of orthologous copies of the retrovirus-like element mys using polymerase chain reaction. We examined these loci in 28 mice collected throughout the P. leucopus species range. Mys insertions were present in only one of the individuals examined at the mys-1 and mys-7 loci. Conversely, the mys-6 element was found in several individuals, but the presence of this element was limited to northern latitudes. Because the
long terminal repeats (LTRs) of a given element are expected to be identical at the time of retrotransposition into the genome,
and to accumulate changes over evolutionary time, within-element LTR sequence comparisons can be used to estimate the relative
age of insertions. Within-element LTR differences are greater in mys-6 than in mys-1 or mys-7. The LTRs from orthologous mys-6 elements of six mice were sequenced. The alignment revealed 13 of the 22 differences between the right and left LTRs that
were shared by all orthologous mys-6 sites, suggesting that relative to its time of insertion into the genome, mys-6 has only recently spread across the northern part of the species range.
Received: 23 January 1996 / Accepted: 24 April 1996 相似文献
19.
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
20.
Microsatellite length variation was investigated at a highly variable microsatellite locus in four species of Apodemus. Information obtained from microsatellite allele sequences was contrasted with allele sizes, which included 18 electromorphs.
Additional analysis of a 400-bp unique sequence in the flanking region identified 26 different haplotype sequences or ``true'
alleles in the sample. Three molecular mechanisms, namely, (1) addition/deletion of repeats, (2) substitutions and indels
in the flanking region, and (3) mutations interrupting the repeat, contributed to the generation of allelic variation. Size
homoplasy can be inferred for alleles within populations, from different populations of the same species, and from different
species. We propose that microsatellite flanking sequences may be informative markers for investigating mutation processes
in microsatellite repeats as well as phylogenetic relationships among alleles, populations, and species.
Received: 3 November 1999 / Accepted: 2 May 2000 相似文献