Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1023-1035 ◽  
Author(s):  
Elena A Salina ◽  
K Yoong Lim ◽  
Ekaterina D Badaeva ◽  
Andrey B Shcherban ◽  
Irina G Adonina ◽  
...  
Keyword(s):  
Copy Number ◽  
Tandem Repeats ◽  
Common Ancestor ◽  
Chromosomal Location ◽  
Phylogenetic Reconstruction ◽  
The Common ◽  
Species Specific ◽  
Phylogenetic Scheme ◽  
Evolutionary Lineages

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.Key words: evolution, RAPD, subtelomeric tandem repeats, Aegilops, wheat, B and G genome.

scholarly journals Comparing the folding landscapes of evolutionarily divergent procaspase-3

2022 ◽  
Author(s):  
Liqi Yao ◽  
Clay Clark
Keyword(s):  
Conformational Change ◽  
Common Ancestor ◽  
Folding Pathway ◽  
Free Energies ◽  
Folding Intermediates ◽  
Effector Caspases ◽  
The Common ◽  
Ph Dependent ◽  
Species Specific ◽  
Dimeric Intermediate

All caspases evolved from a common ancestor and subsequently developed into two general classes, inflammatory or apoptotic caspases. The caspase-hemoglobinase fold has been conserved throughout nearly one billion years of evolution and is utilized for both the monomeric and dimeric subfamilies of apoptotic caspases, called initiator and effector caspases, respectively. We compared the folding and assembly of procaspase-3b from zebrafish to that of human effector procaspases in order to examine the conservation of the folding landscape. Urea-induced equilibrium folding/unfolding of procaspase-3b showed a minimum three-state folding pathway, where the native dimer isomerizes to a partially folded dimeric intermediate, which then unfolds. A partially folded monomeric intermediate observed in the folding landscape of human procaspase-3 is not well-populated in zebrafish procaspase-3b. By comparing effector caspases from different species, we show that the effector procaspase dimer undergoes a pH-dependent conformational change, and that the conformational species in the folding landscape exhibit similar free energies. Together, the data show that the landscape for the caspase-hemoglobinase fold is conserved, yet it provides flexibility for species-specific stabilization or destabilization of folding intermediates resulting in changes in stability. The common pH-dependent conformational change in the native dimer, which yields an enzymatically inactive species, may provide an additional, albeit reversible, mechanism for controlling caspase activity in the cell.

Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 860-867 ◽  
Author(s):  
E A Salina ◽  
O M Numerova ◽  
H Ozkan ◽  
M Feldman
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
First Generation ◽  
Tandem Repeats ◽  
Southern Hybridization ◽  
Homoeologous Pairing ◽  
Genomic Changes ◽  
Intergenomic Recombination ◽  
Copy Numbers

The genomic content of the subtelomeric repeated sequences Spelt1 and Spelt52 was studied by dot, Southern, and in situ hybridization in 11 newly synthesized amphiploids of Aegilops and Triticum, and data were compared with the parental plants. Spelt1 had reduced copy numbers in the first generation of three synthetic amphiploids, but two others did not change; Spelt52 was amplified in nine amphiploids and did not change in two. In the second allopolyploid generation, Spelt1 copy number did not change, whereas there was amplification of Spelt52 in some allopolyploids and decreases in others. Neither allopolyploidy level nor the direction of the cross affected the patterns of change in the newly synthesized amphiploids. Changes did not result from intergenomic recombination because similar alterations were noticed in allopolyploids with and without Ph1, a gene that suppresses homoeologous pairing. No differences in Spelt1 and Spelt52 tandem organization were found by Southern hybridization. The significance of these data are discussed in relation to the establishment of newly formed allopolyploids.Key words: Aegilops, genomic changes, polyploidy, subtelomeric tandem repeats, Triticum, wheat.

scholarly journals A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 711-718 ◽  
Author(s):  
R L Keil ◽  
A D McWilliams
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Copy Number ◽  
Tandem Repeats ◽  
Chromosomal Location ◽  
Specific Factor ◽  
Yeast Saccharomyces Cerevisiae ◽  
Naturally Occurring ◽  
Type Information ◽  
Repeated Genes

Abstract The preservation of sequence homogeneity and copy number of tandemly repeated genes may require specific mechanisms or regulation of recombination. We have identified mutations that specifically affect recombination among natural repetitions in the yeast Saccharomyces cerevisiae. The rrm3 mutation stimulates mitotic recombination in the naturally occurring tandem repeats of the rDNA and copper chelatin (CUP1) genes. This mutation does not affect recombination of several other types of repeated genes tested including Ty elements, mating type information and duplications created by transformation. In addition to stimulating exchange among the multiple CUP1 repeats at their natural chromosomal location, rrm3 also increases recombination of a duplication of CUP1 units present at his4. This suggests that the RRM3 gene may encode a sequence-specific factor that contributes to a global suppression of mitotic exchange in sequences that can be maintained as tandem arrays.

scholarly journals First Description of a Satellite DNA in Manatees’ Centromeric Regions

2021 ◽  
Vol 12 ◽  
Author(s):  
Mirela Pelizaro Valeri ◽  
Guilherme Borges Dias ◽  
Alice Alves do Espírito Santo ◽  
Camila Nascimento Moreira ◽  
Yatiyo Yonenaga-Yassuda ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Extinction Risk ◽  
Homologous Sequence ◽  
Neighbor Joining ◽  
Satellite Dnas ◽  
Trichechus Manatus ◽  
Chromosome Localization ◽  
Future Studies ◽  
The Common ◽  
Species Specific

Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.

ETV6/RUNX1-positive relapses evolve from an ancestral clone and frequently acquire deletions of genes implicated in glucocorticoid signaling

Blood ◽  
2011 ◽  
Vol 117 (9) ◽  
pp. 2658-2667 ◽  
Author(s):  
Lilian Kuster ◽  
Reinhard Grausenburger ◽  
Gerhard Fuka ◽  
Ulrike Kaindl ◽  
Gerd Krapf ◽  
...  
Keyword(s):  
Mismatch Repair ◽  
Copy Number ◽  
Common Ancestor ◽  
Fusion Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Glucocorticoid Signaling ◽  
Dna Copy Number Aberrations ◽  
Insight Into

Abstract Approximately 25% of childhood acute lymphoblastic leukemias carry the ETV6/RUNX1 fusion gene. Despite their excellent initial treatment response, up to 20% of patients relapse. To gain insight into the relapse mechanisms, we analyzed single nucleotide polymorphism arrays for DNA copy number aberrations (CNAs) in 18 matched diagnosis and relapse leukemias. CNAs were more abundant at relapse than at diagnosis (mean 12.5 vs 7.5 per case; P = .01) with 5.3 shared on average. Their patterns revealed a direct clonal relationship with exclusively new aberrations at relapse in only 21.4%, whereas 78.6% shared a common ancestor and subsequently acquired distinct CNA. Moreover, we identified recurrent, mainly nonoverlapping deletions associated with glucocorticoid-mediated apoptosis targeting the Bcl2 modifying factor (BMF) (n = 3), glucocorticoid receptor NR3C1 (n = 4), and components of the mismatch repair pathways (n = 3). Fluorescence in situ hybridization screening of additional 24 relapsed and 72 nonrelapsed ETV6/RUNX1-positive cases demonstrated that BMF deletions were significantly more common in relapse cases (16.6% vs 2.8%; P = .02). Unlike BMF deletions, which were always already present at diagnosis, NR3C1 and mismatch repair aberrations prevailed at relapse. They were all associated with leukemias, which poorly responded to treatment. These findings implicate glucocorticoid-associated drug resistance in ETV6/RUNX1-positive relapse pathogenesis and therefore might help to guide future therapies.

scholarly journals Localization of P elements, copy number regulation, and cytotype determination in Drosophila melanogaster

1990 ◽  
Vol 56 (1) ◽  
pp. 3-14 ◽  
Author(s):  
C. Biémont ◽  
S. Ronsseray ◽  
D. Anxolabéhère ◽  
H. Izaabel ◽  
C. Gautier
Keyword(s):  
Drosophila Melanogaster ◽  
Copy Number ◽  
Chromosomal Location ◽  
Inbred Lines ◽  
P Element ◽  
P Elements ◽  
Left And Right ◽  
Element Activity ◽  
Copy Number Regulation

SummarySeventeen highly-inbred lines of Drosophila melanogaster extracted from an M′ strain (in the P/M system of hybrid dysgenesis) were studied for their cytotype and the number and chromosomal location of complete and defective P elements. While most lines were of M cytotype, three presented a P cytotype (the condition that represses P-element activity) and one was intermediate between M and P. All lines were found to possess K.P elements and only eight to bear full-sized P elements. Only the lines with full-sized P elements showed detectable changes in their P-insertion pattern over generations; their rates of gain and of loss of P-element sites were equal to 0·12 and 0·09 per genome, per generation, respectively. There was no correlation between these two rates within lines, suggesting independent transpositions and excisions in the inbred genomes. The results of both Southern blot analysis and in situ hybridization of probes made from left and right sides of the P element strongly suggested the presence of a putative complete P element in region 1A of the X chromosome in the three lines with a P cytotype; the absence of P copy in this 1A region in lines with an M cytotype, favours the hypothesis that the P element inserted in 1A could play a major role in the P-cytotype determination. Insertion of a defective 2 kb P element was also observed in region 93F in 9 of the 13 M lines. The regulation of the P-element copy number in our lines appeared not to be associated with the ratio of full-length and defective P elements.

scholarly journals Germline-Restricted Chromosome (GRC) is Widespread among Songbirds

2018 ◽  
Author(s):  
Anna A. Torgasheva ◽  
Lyubov P. Malinovskaya ◽  
Kira S. Zadesenets ◽  
Tatyana V. Karamysheva ◽  
Elena A. Kizilova ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Common Ancestor ◽  
Germ Line ◽  
Repetitive Sequences ◽  
Genetic Element ◽  
Selfish Genetic Elements ◽  
Dna Loss ◽  
The Common ◽  
And Function

AbstractThe genome of flying birds, the smallest among amniotes, reflects overweight of the extensive DNA loss over the unrestricted proliferation of selfish genetic elements, resulted in a shortage of repeated sequences and lack of B-chromosomes. The only exception of this rule has been described in zebra finch, which possesses a large germ-line restricted chromosome (GRC), transmitted via oocytes, eliminated from male postmeiotic cells and absent in somatic cell. It is considered as a rarity and its origin, content and function remain unclear. We discovered that all songbirds possess GRC: in various size and genetic content it is present in all fifteen songbird species investigated and absent from germ-line genomes of all eight species of other bird orders examined. Our data based on fluorescent in situ hybridization of DNA probes derived from GRCs of four different Passeri species and their sequencing indicate that the GRCs show low homology between avian species. They contain fragments of the somatic genomes, which include various unique and repetitive sequences. We propose that the GRC has formed in the common ancestor of the extant songbirds and undergone subsequent divergence. GRC presence in the germ line of every songbird studied indicate that it could contain genetic element(s) indispensable for gametogenesis, which are yet to be discovered.

scholarly journals Germline-restricted chromosome (GRC) is widespread among songbirds

2019 ◽  
pp. 201817373 ◽  
Author(s):  
Anna A. Torgasheva ◽  
Lyubov P. Malinovskaya ◽  
Kira S. Zadesenets ◽  
Tatyana V. Karamysheva ◽  
Elena A. Kizilova ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Common Ancestor ◽  
Somatic Cells ◽  
Bird Species ◽  
Supernumerary Chromosome ◽  
Somatic Genome ◽  
The Common ◽  
And Function

An unusual supernumerary chromosome has been reported for two related avian species, the zebra and Bengalese finches. This large, germline-restricted chromosome (GRC) is eliminated from somatic cells and spermatids and transmitted via oocytes only. Its origin, distribution among avian lineages, and function were mostly unknown so far. Using immunolocalization of key meiotic proteins, we found that GRCs of varying size and genetic content are present in all 16 songbird species investigated and absent from germline genomes of all eight examined bird species from other avian orders. Results of fluorescent in situ hybridization of microdissected GRC probes and their sequencing indicate that GRCs show little homology between songbird species and contain a variety of repetitive elements and unique sequences with paralogs in the somatic genome. Our data suggest that the GRC evolved in the common ancestor of all songbirds and underwent significant changes in the extant descendant lineages.

Molecular cytogenetic analysis of supernumerary heterochromatic segments in Rumex acetosa

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 391-397 ◽  
Author(s):  
Fukashi Shibata ◽  
Masahiro Hizume ◽  
Yuzo Kuroki
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
Tandem Repeats ◽  
Mitotic Chromosomes ◽  
Dioecious Plant ◽  
Rumex Acetosa ◽  
Interphase Nuclei ◽  
Heterochromatic Segment ◽  
Molecular Cytogenetic

The dioecious plant Rumex acetosa shows intraspecific karyotype variation, caused by supernumerary heterochromatic segments or DAPI (4',6-diamidino-2 phenylindole)-bands at the ends of the short arms of three pairs of autosomes. A DNA sequence (RAE730) specific to the supernumerary heterochromatic segments was cloned and sequenced. RAE730 was about 730 bp and AT-rich (71% AT-content). Using fluorescence in situ hybridization (FISH), RAE730 was localized in the supernumerary DAPI-positive heterochromatic segments on several mitotic chromosomes and chromocenters in interphase nuclei, but not in the DAPI-bands of Y or B chromosomes. RAE730 was tandemly arranged in the genome, and the copy number varied between plants from 40 000 to 304 000 copies per 2C, corresponding to the relative amount of supernumerary heterochromatic segments per genome. These results indicate that the karyotype variation caused by the supernumerary heterochromatic segment was generated by amplification or reduction of the tandem repeats of RAE730. Key words: Rumex acetosa, repetitive sequence, supernumerary heterochromatic segment, intraspecific karyotype variation, DAPI-band.

scholarly journals Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shauna A. Murray ◽  
Rendy Ruvindy ◽  
Gurjeet S. Kohli ◽  
Donald M. Anderson ◽  
Michael L. Brosnahan
Keyword(s):  
Copy Number ◽  
A Priori ◽  
Full Range ◽  
Paralytic Shellfish Poisoning ◽  
Shellfish Poisoning ◽  
Alexandrium Catenella ◽  
Paralytic Shellfish ◽  
Species Specific ◽  
Group 1

Abstract Alexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L−1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.

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