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1.
T. H. N. Ellis S. J. Poyser M. R. Knox A. V. Vershinin M. J. Ambrose 《Molecular & general genetics : MGG》1998,260(1):9-19
A sample of 15 cultivars and 56 Pisum accessions from the JIC germplasm core collection has been studied using a modification of the SSAP (sequence-specific amplification
polymorphisms) technique; the specific primer was designed to correspond to the polypurine tract (PPT) of PDR1, a Ty1-copia group retrotransposon of pea. Most of these SSAP products were shown to be PDR1 derived. The PDR1 SSAP markers are more informative than previously studied AFLP or RFLP markers and are distributed throughout the genome.
Their pattern of variation makes them ideal for integrating genetic maps derived from related crosses. Data sets obtained
with AFLP and PDR1 SSAP markers were used to construct neighbour-joining trees and for principal component analysis. These data sets give greater
resolution than hitherto available for the characterisation of variation within Pisum, showing that the genus has three main groups: P. fulvum, P. abyssinicum and all other Pisum spp. P. abyssinicum is not a subgroup of cultivated P. sativum, as was previously thought, but has probably been domesticated independently. Modern cultivars are shown to form a single
group within Pisum as a whole.
Received: 21 April 1998 / Accepted: 9 June 1998 相似文献
2.
Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum 总被引:3,自引:0,他引:3
Pearce SR Knox M Ellis TH Flavell AJ Kumar A 《Molecular & general genetics : MGG》2000,263(6):898-907
The variation in transposition history of different Ty1-copia group LTR retrotransposons in the species lineages of the Pisum genus has been investigated. A heterogeneous population of Ty1-copia elements was isolated by degenerate PCR and two of these (Tps12 and Tps19) were selected on the basis of their copy number and sequence conservation between closely related species for further in-depth
study of their transpositional history in Pisum species. The insertional polymorphism of these elements and the previously characterised PDR1 element was studied by sequence-specific amplification polymorphism (SSAP). Each of these elements reveals a unique transpositional
history within 55 diverse Pisum accessions. Phylogenetic trees based on the SSAP data show that SSAP markers for individual elements are able to resolve
different species lineages within the Pisum genus. Finally, the SSAP data from all of these retrotransposon markers were combined to reveal a detailed picture of the
intra and inter-species relationships within Pisum.
Received: 23 January 2000 / Accepted: 24 March 2000 相似文献
3.
Jaroslava Cieslarová Pavel Hanáček Eva Fialová Miroslav Hýbl Petr Smýkal 《Journal of applied genetics》2011,52(4):391-401
Microsatellites, or simple sequence repeats (SSRs) are widespread class of repetitive DNA sequences, used in population genetics,
genetic diversity and mapping studies. In spite of the SSR utility, the genetic and evolutionary mechanisms are not fully
understood. We have investigated three microsatellite loci with different position in the pea (Pisum sativum L.) genome, the A9 locus residing in LTR region of abundant retrotransposon, AD270 as intergenic and AF016458 located in
5′untranslated region of expressed gene. Comparative analysis of a 35 pair samples from seven pea varieties propagated by
single-seed descent for ten generations, revealed single 4 bp mutation in 10th generation sample at AD270 locus corresponding
to stepwise increase in one additional ATCT repeat unit. The estimated mutation rate was 4.76 × 10-3 per locus per generation, with a 95% confidence interval of 1.2 × 10-4 to 2.7 × 10-2. The comparison of cv. Bohatyr accessions retrieved from different collections, showed intra-, inter-accession variation
and differences in flanking and repeat sequences. Fragment size and sequence alternations were also found in long term in
vitro organogenic culture, established at 1983, indicative of somatic mutation process. The evidence of homoplasy was detected
across of unrelated pea genotypes, which adversaly affects the reliability of diversity estimates not only for diverse germplasm
but also highly bred material. The findings of this study have important implications for Pisum phylogeny studies, variety identification and registration process in pea breeding where mutation rate influences the genetic
diversity and the effective population size estimates. 相似文献
4.
T. H. N. Ellis S. J. Poyser M. R. Knox A. V. Vershinin M. J. Ambrose 《Molecular genetics and genomics : MGG》1998,260(1):9-19
A sample of 15 cultivars and 56 Pisum accessions from the JIC germplasm core collection has been studied using a modification of the SSAP (sequence-specific amplification polymorphisms) technique; the specific primer was designed to correspond to the polypurine tract (PPT) of PDR1, a Ty1-copia group retrotransposon of pea. Most of these SSAP products were shown to be PDR1 derived. The PDR1 SSAP markers are more informative than previously studied AFLP or RFLP markers and are distributed throughout the genome. Their pattern of variation makes them ideal for integrating genetic maps derived from related crosses. Data sets obtained with AFLP and PDR1 SSAP markers were used to construct neighbour-joining trees and for principal component analysis. These data sets give greater resolution than hitherto available for the characterisation of variation within Pisum, showing that the genus has three main groups: P. fulvum, P. abyssinicum and all other Pisum spp. P. abyssinicum is not a subgroup of cultivated P. sativum, as was previously thought, but has probably been domesticated independently. Modern cultivars are shown to form a single group within Pisum as a whole. 相似文献
5.
To better understand the genetic diversity of the wild relatives of rice (Oryza sativa L.) in the O. officinalis species complex repetitive DNA markers were obtained from the diploid species of this complex. One cloned sequence from O. eichingeri gave intense hybridization signals with all species of the O. officinalis complex. This 242 bp clone, named pOe.49, has a copy number from 0.9 to 4.0 × 104 in diploid species of this complex. Analysis of the primary structure and database searches revealed homology of pOe.49 to
a number of sequences representing part of the integrase coding domain of retroviruses and gypsy-like retrotransposons. Sequencing of specific PCR products confirmed that pOe.49 is part of a gypsy-like retrotransposon. RFLP analysis was used to study the genomic organisation of pOe.49 among 30 accessions of the O. officinalis complex using 10 restriction enzymes. Diversity analysis based on 120 polymorphic fragments obtained from the RFLP assay
grouped the O. officinalis complex accessions by genome, species and eco-geographic groups. The results suggest that, with further characterization,
this retrotransposon-like DNA sequence may be useful for phylogenetic analysis of species in the O. officinalis complex.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
6.
Lessard PA O'Brien XM Ahlgren NA Ribich SA Sinskey AJ 《Applied microbiology and biotechnology》1999,52(6):811-819
To develop a transposable element-based system for mutagenesis in Rhodococcus, we used the sacB gene from Bacillus subtilis to isolate a novel transposable element, IS1676, from R. erythropolis SQ1. This 1693 bp insertion sequence is bounded by imperfect (10 out of 13 bp) inverted repeats and it creates 4 bp direct
repeats upon insertion. Comparison of multiple insertion sites reveals a preference for the sequence 5′-(C/T)TA(A/G)-3′ in
the target site. IS1676 contains a single, large (1446 bp) open reading frame with coding potential for a protein of 482 amino acids. IS1676 may be similar to an ancestral transposable element that gave rise to repetitive sequences identified in clinical isolates
of Mycobacteriumkansasii. Derivatives of IS1676 should be useful for analysis of Rhodococcus strains, for which few other genetic tools are currently available.
Received: 1 April 1999 / Received revision: 6 July 1999 / Accepted: 1 August 1999 相似文献
7.
Y. Hisatomi K. Hanada S. Iida 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(7):1049-1056
Transposable elements have often been discovered as new insertion sequences in known genes, and minisatellites are often
employed as molecular markers in diagnostic and mapping studies. We compared the genes for flower pigmentation in a line of
the common morning glory bearing fully colored flowers with those in two anthocyanin
flaked
mutable lines producing variegated flowers and found RFLPs at the region of the ANS gene for anthocyanin biosynthesis. The DNA rearrangements detected by the RFLPs are due to integration of a novel type of
minisatellite, MiniSip1, having a long LTR retrotransposon, RTip1, inserted in the mutable lines. The structural analysis of the rearranged region revealed that the 12.4-kb RTip1 element is flanked by 5-bp target duplications within the MiniSip1 sequence and contains two LTR sequences of about 590 bp, a primer binding site for tRNALys, a typical polypurine tract and another new type of minisatellite, MiniSip2. Since no long open reading frame corresponding to the gag and pol genes was found, RTip1 appears to be a defective Ty3/gypsy-like element. Interestingly, the 269-bp-long MiniSip1 element comprises two alternating motifs of 41 bp and 19 bp, whereas the 962 bp long MiniSip2 element consists of two partially alternating motifs of 86 bp and 90 bp which are partially homologous to each other. Possible
evolutionary processes that may have generated the rearranged structure at the ANS gene region are also discussed.
Received: 25 April 1997 / Accepted: 16 May 1997 相似文献
8.
9.
An Assessment of the Phylogenetic Relationship Among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5S rRNA Intergenic Spacers 总被引:4,自引:0,他引:4
5S rRNA intergenic spacers were amplified from two elite sugarcane (Saccharumhybrids) cultivars and their related taxa by polymerase chain reaction (PCR) with 5S rDNA consensus primers. Resulting PCR
products were uniform in length from each accession but exhibited some degree of length variation among the sugarcane accessions
and related taxa. These PCR products did not always cross hybridize in Southern blot hybridization experiments. These PCR
products were cloned into a commercial plasmid vector PCR™ 2.1 and sequenced. Direct sequencing of cloned PCR products revealed
spacer length of 231–237 bp for S. officinarum, 233–237 for sugarcane cultivars, 228–238 bp for S. spontaneum, 239–252 bp for S. giganteum, 385–410 bp for Erianthusspp., 226–230 bp for Miscanthus sinensisZebra, 206–207 bp for M. sinensisIMP 3057, 207–209 bp for Sorghum bicolor, and 247–249 bp for Zea mays. Nucleotide sequence polymorphism were found at both the segment and single nucleotide level. A consensus sequence for each
taxon was obtained by Align X. Multiple sequences were aligned and phylogenetic trees constructed using Align X, CLUSTAL and
DNAMAN programs. In general, accessions of the following taxa tended to group together to form distinct clusters: S. giganteum, Erianthusspp., M. sinensis, S. bicolor, and Z. mays. However, the two S. officinarumclones and two sugarcane cultivars did not form distinct clusters but interrelated within the S. spontaneumcluster. The disclosure of these 5S rRNA intergenic spacer sequences will facilitate marker-assisted breeding in sugarcane.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
10.
N. Uematsu C. Matsuoka Y. Agemizu E. Nagoshi K. Yamamoto 《Molecular & general genetics : MGG》1999,261(3):523-529
The chromosomal tonB gene of Escherichia coli was used as a target for the detection of spontaneous deletion mutations. The deletions were isolated in both recA
+ and recA
− cells, and mutants carrying large deletions were identified because they also lacked part or all of the trp operon. The frequencies of tonB-trp deletion were 1.79 × 10−9 and 1.09 × 10−9 for recA
+ and recA
− cells, respectively. We analyzed 12 deletions from recA
+ and 10 from recA
− cells by cloning and direct sequencing. The deletions ranged in size from 5612 bp to 15142 bp for recA
+ and from 5428 bp to 13289 for recA
− cells. Three deletions from recA
+ cells and five deletions from recA
− cells were found to have occurred between short sequence repeats at the termini of the deletion, leaving one copy of the
repeat in the mutant sequence. Seven deletions from recA
+ cells and three deletions from recA
− cells did not have repeats at their termini; in these cases, the DNA sequences that are adjacent to the deletion termini
in the wild-type are characterized by short (2–4 bp) repeats. From these results, a model is presented for the generation
of deletion mutations which involves formation of an asymmetric crossover mediated by repeated sequences of 2- to 4-bp.
Received: 14 September 1998 / Accepted: 22 December 1998 相似文献
11.
12.
E. Grosselindemann M. Robertson J. A. Wilmer P. M. Chandler 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(8):1186-1192
The electrophoretic patterns of dehydrins extracted from mature seeds of a range of pea (Pisum) species revealed extensive variation in dehydrin polypeptide mobility. Variation was also observed among lines of P. sativum. Crosses between lines with different dehydrin electrophoretic patterns produced F1 seeds with additive patterns, and segregation in the F2 generation was consistent with a 1 : 2 : 1 ratio, indicating allelic variation at each of two dehydrin loci (Dhn2, Dhn3). Genetic linkage was observed between Dhn2 and Dhn3, and the segregation ratios indicated preferential transmission of one allele at the Dhn3 locus. Dehydrin cDNA clones were characterised that encoded the allelic variants at Dhn2 and Dhn3. Their deduced amino-acid sequences were very similar to each other as well as to the product of the Dhn1 locus reported previously. Comparisons were made between the sequences of allelic variants at a single locus, and between
the products of different loci. Differences in the electrophoretic mobilities between allelic variants at Dhn2 and Dhn3 were associated with differences in polypeptide length resulting principally from tandem duplications of 21 (Dhn2) or 24 (Dhn3) amino-acid residues. These duplications accounted for much of the difference in length between dehydrins encoded by the
different loci. The conserved core of one of the duplicated regions varied in copy number, and small insertions/deletions
of amino acids near this core also contributed to length variation both between allelic forms and between loci. Dehydrins
possess characteristic highly conserved amino-acid sequence motifs, yet vary considerably in length. Mechanisms involving
sequence duplication appear to be responsible for generating the length differences observed between allelic variants as well
as between the products of different loci.
Received: 12 June 1997 / Accepted: 29 October 1997 相似文献
13.
M. Vukich A. H. Schulman T. Giordani L. Natali R. Kalendar A. Cavallini 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(6):1027-1038
The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied for the first time within the genus Helianthus to assess intraspecific variability based on retrotransposon sequences among 36 wild accessions and 26 cultivars of Helianthus annuus L., and interspecific variability among 39 species of Helianthus. Two groups of LTRs, one belonging to a Copia-like retroelement and the other to a putative retrotransposon of unknown nature (SURE) have been isolated, sequenced and primers were designed to obtain IRAP fingerprints. The number of polymorphic bands in
H. annuus wild accessions is as high as in Helianthus species. If we assume that a polymorphic band can be related to a retrotransposon insertion, this result suggests that retrotransposon
activity continued after Helianthus speciation. Calculation of similarity indices from binary matrices (Shannon’s and Jaccard’s indices) show that variability is reduced
among domesticated H. annuus. On the contrary, similarity indices among Helianthus species were as large as those observed among wild H. annuus accessions, probably related to their scattered geographic distribution. Principal component analysis of IRAP fingerprints
allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned. 相似文献
14.
15.
Hayashi H Takehara M Hattori T Kimura T Karita S Sakka K Ohmiya K 《Applied microbiology and biotechnology》1999,51(3):348-357
A 5.7-kbp region of the Clostridium thermocellum F1 DNA was sequenced and found to contain two contiguous and highly homologous xylanase genes, xynA and xynB. The xynA gene encoding the xylanase XynA consists of 2049 bp and encodes a protein of 683 amino acids with a molecular mass of 74 511 Da,
and the xynB gene encoding the xylanase XynB consists of 1371 bp and encodes a protein of 457 amino acids with a molecular mass of 49 883 Da.
XynA is a modular enzyme composed of a typical N-terminal signal peptide and four domains in the following order: a family-11
xylanase domain, a family-VI cellulose-binding domain, a dockerin domain, and a NodB domain. XynB exhibited extremely high
overall sequence homology with XynA (identity 96.9%), while lacking the NodB domain present in the latter. These facts suggested
that the xynA and xynB genes originated from a common ancestral gene through gene duplication. XynA was purified from a recombinant Escherichia coli strain and characterized. The purified enzyme was highly active toward xylan; the specific activity on oat-spelt xylan was
689 units/mg protein. Immunological and zymogram analyses suggested that XynA and XynB are components of the C. thermocellum F1 cellulosome.
Received: 21 September 1998 / Received revision: 30 October 1998 / Accepted: 29 November 1998 相似文献
16.
BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.) 总被引:5,自引:0,他引:5
17.
Moisy C Blanc S Merdinoglu D Pelsy F 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,116(5):671-682
Structural variability of Tvv1, a grapevine retrotransposon Ty1 copia-like family, was investigated within the grape genome and the canonical sequence of Tvv1 determined. Then, two remarkable elements, Tvv1-Δ3001 and Tvv1-Δ3640, which had suffered large deletions 3,001 bp and 3,460 bp in length of their coding sequences were compared to the
canonical copy. In both deleted elements, the deletion breakpoint was characterized by a stretch 13 bp-long in Tvv1-Δ3001 and 11 bp-long in Tvv1-Δ3640 found duplicated in the canonical copy at each bound of the deleted regions. Tvv1-Δ3001 and Tvv1-Δ3460 were both shown to be unique copies fixed at a single locus in the grapevine genome. Their presence was very variable
in a set of 58 varieties and wild vines. These elements have most likely been dispersed through natural intermixing after
their initial insertion whose chronology was estimated. The model that we propose to explain the structure of Tvv1-Δ3001 and Tvv1-Δ3640, implies illegitimate recombination involving template switching between two RNA molecules co-packaged in the VLP prior
to the integration of the deleted daughter copy into the host genome. 相似文献
18.
A transposable element, Flipper, was isolated from the phytopathogenic fungus Botrytis cinerea. The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. The Flipper
sequence is 1842 bp long with perfect inverted terminal repeats (ITRs) of 48 bp and an open reading frame (ORF) of 533 amino
acids, potentially encoding for a transposase; the element is flanked by the dinucleotide TA. The encoded protein is very
similar to the putative transposases of three elements from other phytopathogenic fungi, Fot1 from Fusarium oxysporum, and Pot2 and MGR586 from Magnaporthe grisea. The number of Flipper elements in strains of B. cinerea varied from 0 to 20 copies per genome. Analysis of the descendants of one cross showed that the segregation ratio of Flipper
elements was 2:2 and that the copies were not linked.
Received: 4 December 1996 / Accepted: 21 January 1997 相似文献
19.
Ty3/gypsy-type LTR-retrotransposons have been found only in lily and maize but not in cryptogam. In fernAdiantum, we recently found a full-lengthTy3/gypsy-type LTR-retrotransposon (ARET-1; 8284 bp). This retrotransposon has both 5′ and 3′ LTRs (1.2 kb), a primer binding site, a polypurine tract, and an RNA binding
motif and its domain arrangement in thepol region is the same as that ofTy3/gypsy-type retrotransposon. These results suggest thatTy3/gypsy-type retrotransposons are widespread among vascular plants.
The nucleotide sequence data reported will appear in the EMBL, DDBJ and GenBank Nucleotide Sequence Databases under the accession
number AB003364. 相似文献