Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 272-277 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
G Segal ◽  
S Abbo ◽  
M Rodova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Frequency ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Chromosome Differentiation ◽  
Genomic Changes ◽  
Parental Lines ◽  
Copy Dna ◽  
Homoeologous Chromosomes ◽  
Specific Sequences

We recently reported that allopolyploid formation in wheat was accompanied by rapid nonrandom elimination of specific low-copy, noncoding DNA sequences. These sequences occur in all diploid progenitors but are chromosome- or genome-specific at the polyploid level. To further investigate this phenomenon, we studied nine of these sequences, six chromosome-specific sequences and three genome-specific sequences, all isolated from common wheat. The various sequences were hybridized to DNA derived from nine newly synthesized amphiploids at different ploidy levels and to DNA from their parental lines. Although sequences homologous to the probes occur in all parental lines, a nonrandom loss of hybridization fragments was found at a high frequency in all amphiploids studied. In addition, a "loss/gain" of a hybridization fragment(s) was noticed in some of the amphiploids at lower frequency. Neither the type nor the frequency of changes was affected by intergenomic recombination or DNA methylation. It is suggested that rapid genomic changes culminated in a "programmed" pattern of elimination and (or) modification of specific low-copy DNA sequences following allopolyploidization. These events augmented the differentiation of homoeologous chromosomes, thus providing the physical basis for the diploid-like cytological behavior of polyploid wheat.Key words: wheat, allopolyploidy, genome evolution, chromosome- or genome-specific sequences, sequence elimination, homoeologous chromosome differentiation.

Rapid genomic changes in newly synthesized amphiploids ofTriticumandAegilops. II. Changes in low-copy coding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 535-542 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
M Feldman
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Gene Dosage ◽  
Restriction Enzymes ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Coding Sequences ◽  
Genomic Changes ◽  
Cdna Sequences ◽  
Specific Sequences

We recently reported that formation of allopolyploid wheat was accompanied by rapid nonrandom changes in low-copy noncoding DNA sequences. In this report we show that following allopolyploidization, changes also occurred in coding sequences. Genomic DNA of nine different newly synthesized amphiploids of different ploidy levels and their parental lines was digested with five restriction enzymes and probed with 43 coding sequences. The sequences, 19 genomic and 24 cDNA sequences, are group (homoeologous) specific and represent the proximal and distal regions of the short and long arms of the seven homoeologous groups of the Triticeae. We revealed three types of changes: disappearance of a parental hybridization fragment(s), appearance of a novel fragment(s), and simultaneous disappearance of a parental fragment(s) and appearance of a novel fragment(s). No elimination of sequences took place, since in every sequence studied the parental hybridization fragments were present in at least one of the enzyme digests. Variations in pattern among individual plants of the same amphiploid, as well as between several synthetic and natural amphiploids, indicated that at least some of the genomic changes occurred at random. Intergenomic recombination was not the cause of the observed changes. Evidence was obtained, however, that changes were also brought about by DNA methylation. Methylation may cause inactivation of genes or modify their expression levels in some of the newly synthesized amphiploid plants, leading to genetic diploidization and gene-dosage compensation and thus increasing variation among individuals.Key words: wheat, allopolyploidy, DNA methylation, genetic diploidization, genome evolution, group (homoeologous) specific sequences.

scholarly journals Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1381-1387 ◽  
Author(s):  
Moshe Feldman ◽  
Bao Liu ◽  
Gregorio Segal ◽  
Shahal Abbo ◽  
Avraham A Levy ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Tetraploid Wheat ◽  
Diploid Species ◽  
Noncoding Dna ◽  
Polyploid Wheat ◽  
Genomic Changes ◽  
Group I ◽  
Group Ii ◽  
Homoeologous Chromosomes

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, lowcopy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.

Rapid cytological diploidization in newly formed allopolyploids of the wheat (Aegilops-Triticum) group

Genome ◽  
2009 ◽  
Vol 52 (11) ◽  
pp. 926-934 ◽  
Author(s):  
Hakan Ozkan ◽  
Moshe Feldman
Keyword(s):  
Chromosome Pairing ◽  
Dna Sequences ◽  
Meiotic Metaphase ◽  
Epigenetic Changes ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Seed Fertility ◽  
Positive Linear Relationship ◽  
Competitive Species ◽  
Homoeologous Chromosomes

Recent studies in the genera Aegilops and Triticum showed that allopolyploid formation triggers rapid genetic and epigenetic changes that lead to cytological and genetic diploidization. To better understand the consequences of cytological diploidization, chromosome pairing and seed fertility were studied in S1, S2, and S3generations of 18 newly formed allopolyploids at different ploidy levels. Results showed that bivalent pairing at first meiotic metaphase was enhanced and seed fertility was improved during each successive generation. A positive linear relationship was found between increased bivalent pairing, improved fertility, and elimination of low-copy noncoding DNA sequences. These findings support the conclusion that rapid elimination of low-copy noncoding DNA sequences from one genome of a newly formed allopolyploid, different sequences from different genomes, is an efficient way to quickly augment the divergence between homoeologous chromosomes and thus bring about cytological diploidization. This facilitates the rapid establishment of the raw allopolyploids as successful, competitive species in nature.

Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 272-277 ◽  
Author(s):  
B. Liu ◽  
J.M. Vega ◽  
G. Segal ◽  
S. Abbo ◽  
M. Rodova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Noncoding Dna ◽  
Genomic Changes

scholarly journals Congruity of the Polymorphisms in the Expressed and Noncoding Parts of the Gli-B1 Locus in Common Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1510
Author(s):  
Yulia Popovych ◽  
Sabina Chebotar ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
Laura Pascual ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Evolutionary Significance ◽  
Sequence Length ◽  
Noncoding Dna ◽  
Important Region ◽  
Novel Variants ◽  
Specific Sequences

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 locus. A congruity was established between this polymorphism, allelic sets of the Gli-B1-produced gliadins (especially of the electrophoretic mobility in acid gels of the encoded γ-gliadin) and the presence in the wheat genotype of the Gli-B5b + Rg-1 allelic combination. Six different alleles at the Gli-B1 locus encoding an identical γ-gliadin produced a PCR sequence of about 400 bp (GliB1.1). Nine Gli-B1d-carrying genotypes from four countries produced an identical sequence of about 409 bp (GliB1.2), while three cultivars with Gli-B1h and four with Gli-B1b produced three and two specific sequences, respectively, of slightly different length. Allele Gli-B1j might be the result of recombination between coding and noncoding DNA sequences within the Gli-B1 locus. These observations imply that genetic diversity of the agriculturally important region of chromosome 1B marked by variants of the Gli-B1 locus is rather limited among common wheat cultivars of the 20th century, specifically to eight principal versions. These might have been incorporated into common wheat from diverged genotypes of diploid donor(s), and, due to the scarcity of recombination, subsequently maintained relatively intact. As well as its evolutionary significance, this information is of potential use in wheat breeding and we consider it likely that novel variants of the Gli-B1 locus will be found in hitherto unstudied germplasm.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Telomeric DNA sequences in beetle taxa vary with species richness

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniela Prušáková ◽  
Vratislav Peska ◽  
Stano Pekár ◽  
Michal Bubeník ◽  
Lukáš Čížek ◽  
...  
Keyword(s):  
Species Richness ◽  
Dna Sequences ◽  
Genome Instability ◽  
Telomeric Sequence ◽  
Dna Repeats ◽  
Telomeric Dna ◽  
Common Pattern ◽  
Telomeric Sequences ◽  
Genomic Changes ◽  
Protective Structures

AbstractTelomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

1995 ◽  
Vol 51 (5) ◽  
pp. 5084-5091 ◽  
Author(s):  
S. V. Buldyrev ◽  
A. L. Goldberger ◽  
S. Havlin ◽  
R. N. Mantegna ◽  
M. E. Matsa ◽  
...  
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Noncoding Dna ◽  
Range Correlation ◽  
Correlation Properties

Parasites in Antarctic krill guts inferred from DNA sequences

2019 ◽  
Vol 31 (1) ◽  
pp. 16-22 ◽  
Author(s):  
Alison C. Cleary ◽  
Maria C. Casas ◽  
Edward G. Durbin ◽  
Jaime Gómez-Gutiérrez
Keyword(s):  
Dna Sequences ◽  
High Frequency ◽  
Dna Analysis ◽  
Antarctic Krill ◽  
Euphausia Superba ◽  
Gut Contents ◽  
The West ◽  
West Antarctic ◽  
Wide Range

AbstractThe keystone role of Antarctic krill,Euphausia superbaDana, in Southern Ocean ecosystems, means it is essential to understand the factors controlling their abundance and secondary production. One such factor that remains poorly known is the role of parasites. A recent study of krill diet using DNA analysis of gut contents provided a snapshot of the parasites present within 170E. superbaguts in a small area along the West Antarctic Peninsula. These parasites includedMetschnikowiaspp. fungi,Haptoglossasp. peronosporomycetes,LankesteriaandParalecudinaspp. apicomplexa,Stegophorussp. nematodes, andPseudocolliniaspp. ciliates. Of these parasites,Metschnikowiaspp. fungi andPseudocolliniaspp. ciliates had previously been observed inE. superba, as had other genera of apicomplexans, though notLankesteriaandParalecudina.In contrast, nematodes had previously only been observed in eggs ofE. superba, and there are no literature reports of peronosporomycetes in euphausiids.Pseudocolliniaspp., parasitoids which obligately kill their host, were the most frequently observed infection, with a prevalence of 12%. The wide range of observed parasites and the relatively high frequency of infections suggest parasites may play a more important role than previously acknowledged inE. superbaecology and population dynamics.

NONSTRUCTURAL CHROMOSOME DIFFERENTIATION AMONG WHEAT CULTIVARS, WITH SPECIAL REFERENCE TO DIFFERENTIATION OF CHROMOSOMES IN RELATED SPECIES

Genetics ◽  
1981 ◽  
Vol 97 (2) ◽  
pp. 391-414
Author(s):  
Jan Dvořák ◽  
Patrick E McGuire
Keyword(s):  
Chinese Spring ◽  
Structural Changes ◽  
Wheat Cultivar ◽  
Chromosome Complement ◽  
Triticum Aestivum L ◽  
Substitution Lines ◽  
Structural Differentiation ◽  
Chromosome Differentiation ◽  
Mother Cells ◽  
Homoeologous Chromosomes

ABSTRACT Wheat cultivar Chinese Spring (Triticum aestivum L. em. Thell.) was crossed with cultivars Hope, Cheyenne and Timstein. In all three hybrids, the frequencies of pollen mother cells (PMCs) with univalents at metaphase I (MI) were higher than those in the parental cultivars. No multivalents were observed in the hybrids, indicating that the cultivars do not differ by translocations. Thirty-one Chinese Spring telosomic lines were then crossed with substitution lines in which single chromosomes of the three cultivars were substituted for their Chinese Spring homologues. The telosomic lines were also crossed with Chinese Spring. Data were collected on the frequencies (% of PMCs) of pairing of the telesomes with their homologues at MI and the regularity of pairing of the remaining 20 pairs of Chinese Spring chromosomes in the monotelodisomics obtained from these crosses. The reduced MI pairing in the intercultivar hybrids was caused primarily by chromosome differentiation, rather than by specific genes. Because the differentiation involved a large part of the chromosome complement in each hybrid, it was concluded that it could not be caused by structural changes such as inversions or translocations. In each case, the differentiation appeared to be unevenly distributed among the three wheat genomes. It is proposed that the same kind of differentiation, although of greater magnitude, differentiates homoeologous chromosomes and is responsible, together with structural differentiation, for poor chromosome pairing in interspecific hybrids.

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