scholarly journals Repetitive sequences originating from the centromere constitute large-scale heterochromatin in the telomere region in the siamang, a small ape

Heredity ◽  
2012 ◽  
Vol 109 (3) ◽  
pp. 180-187 ◽  
Author(s):  
A Koga ◽  
Y Hirai ◽  
T Hara ◽  
H Hirai
Keyword(s):  
Large Scale ◽  
Repetitive Sequences ◽  
Telomere Region

scholarly journals Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences

2010 ◽  
Vol 2010 ◽  
pp. 1-7
Author(s):  
Myron Peto ◽  
David M. Grant ◽  
Randy C. Shoemaker ◽  
Steven B. Cannon
Keyword(s):  
Quality Control ◽  
Binding Energy ◽  
Dna Binding ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Soybean Genome ◽  
Small Scale ◽  
Whole Genome ◽  
Soybean Chromosome ◽  
A Genome

Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules.

scholarly journals A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata)

2020 ◽  
Author(s):  
Beate Nürnberger ◽  
Stuart J.E. Baird ◽  
Dagmar Čížková ◽  
Anna Bryjová ◽  
Austin B. Mudd ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Large Scale ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Secondary Contact ◽  
Gene Pools ◽  
Hybrid Zones ◽  
Chromosome 5 ◽  
Bombina Bombina

AbstractHybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses. The enrichment targets were selected from a draft assembly of the B. variegata genome, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Large-scale synteny between Bombina and Xenopus tropicalis supports the resulting linkage map. By assessing the sex of late-stage F2 tadpoles from histological sections, we also identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety, suggestive of an XY sex determination mechanism. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

scholarly journals Transcription of a Donor Enhances Its Use during Double-Strand Break-Induced Gene Conversion in Human Cells

2006 ◽  
Vol 26 (8) ◽  
pp. 3098-3105 ◽  
Author(s):  
Ezra Schildkraut ◽  
Cheryl A. Miller ◽  
Jac A. Nickoloff
Keyword(s):  
Gene Conversion ◽  
Genome Stability ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Indirect Evidence ◽  
Strand Break ◽  
Strand Breaks ◽  
Homologous Chromosomes ◽  
Donor Choice ◽  
Donor Preference

ABSTRACT Homologous recombination (HR) mediates accurate repair of double-strand breaks (DSBs) but carries the risk of large-scale genetic change, including loss of heterozygosity, deletions, inversions, and translocations. Nearly one-third of the human genome consists of repetitive sequences, and DSB repair by HR often requires choices among several homologous repair templates, including homologous chromosomes, sister chromatids, and linked or unlinked repeats. Donor preference during DSB-induced gene conversion was analyzed by using several HR substrates with three copies of neo targeted to a human chromosome. Repair of I-SceI nuclease-induced DSBs in one neo (the recipient) required a choice between two donor neo genes. When both donors were downstream, there was no significant bias for proximal or distal donors. When donors flanked the recipient, we observed a marked (85%) preference for the downstream donor. Reversing the HR substrate in the chromosome eliminated this preference, indicating that donor choice is influenced by factors extrinsic to the HR substrate. Prior indirect evidence suggested that transcription might increase donor use. We tested this question directly and found that increased transcription of a donor enhances its use during gene conversion. A preference for transcribed donors would minimize the use of nontranscribed (i.e., pseudogene) templates during repair and thus help maintain genome stability.

scholarly journals Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 312
Author(s):  
Veronika Borůvková ◽  
W. Mike Howell ◽  
Dominik Matoulek ◽  
Radka Symonová
Keyword(s):  
Large Scale ◽  
Open Space ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Chromosome Size ◽  
Vertebrate Genome ◽  
Fish Cytogenetics ◽  
Large Variability ◽  
The Relationship ◽  
Chromosome Level

Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.

scholarly journals Content of and interactions between repetitive elements in programmatically eliminated chromosomes of the sea lamprey (Petromyzon marinus)

2019 ◽  
Author(s):  
Vladimir A. Timoshevskiy ◽  
Nataliya Y. Timoshevskaya ◽  
Jeramiah J. Smith
Keyword(s):  
Large Scale ◽  
Genome Rearrangement ◽  
Petromyzon Marinus ◽  
Repetitive Sequences ◽  
Sea Lamprey ◽  
Repetitive Elements ◽  
Integrative Approach ◽  
Vertebrate Species ◽  
Repeat Content ◽  
Specific Subset

ABSTRACTThe sea lamprey (Petromyzon marinus) is one of few vertebrate species that is known to reproducibly eliminate large fractions of its genome during normal embryonic development. In lamprey, elimination events are initiated at the 6thembryonic cleavage and result in the loss of ∼20% of an embryo’s genomic DNA from essentially all somatic cell lineages (these same sequences are retained in the germline). This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination acts as a permanent silencing mechanism that prevents the somatic expression of a specific subset of “germline” genes. However, reconstruction of eliminated regions has proven challenging due to the complexity of the lamprey karyotype (84 small pairs of somatic chromosomes and ∼100 pairs of germline chromosomes), the exceedingly high repeat content of the genome and even higher repeat content of eliminated fragments.We applied an integrative approach aimed at further characterization of the large-scale structure of eliminated segments, including: 1)in silicoidentification of germline-enriched repeats; mapping the chromosomal location of specific repetitive sequences in germline metaphases, and verification of repeat specificity to eliminated chromosomes by 3D DNA/DNA-hybridization to embryonic lagging anaphases. Our integrative approach resulted in the discovery of multiple highly abundant repetitive elements that are found exclusively on the eliminated (germline-specific) chromosomes which in turn permitted the identification of 12 individual chromosomes that are programmatically eliminated during early embryogenesis. The fidelity of germline-specific repetitive elements and their distinctive patterning in elimination anaphases are taken as evidence that these sequences might contribute to the specific targeting of chromosomes for elimination and possibly in molecular interactions that mediate their decelerated poleward movement in chromosome elimination anaphases, isolation from the primary nuclei and eventual degradation.AUTHOR SUMMARYEpigenetic silencing methods provide a means of precisely restricting gene expression while maintaining the integrity of the genomic template that encodes this information, and are employed by diverse species throughout the tree of life. Programmed genome rearrangement (PGR) represents a parallel approach that maintains genome integrity across generations but alters the genomes of cells within an organism. To better resolve elimination events that take place during PGR in the sea lamprey (one of few vertebrate species known to undergo large scale PGR) we sought to identify sequences that define specific eliminated chromosomes. Using computational predictions and cytogenetic validation, we identified six new repetitive elements that are restricted to the eliminated chromosomes and permit the identification of twelve distinct eliminated chromosomes. Analysis of these repeats in meiotic testes and in embryos sampled during the process of elimination shows that these repeats localize to specific subcellular regions, and suggest a potential role of these repetitive elements in targeting chromosomes for silencing via elimination.

scholarly journals Genome Survey Sequencing of Betula platyphylla

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 826 ◽  
Author(s):  
Sui Wang ◽  
Su Chen ◽  
Caixia Liu ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Genome Size ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Northern China ◽  
Third Generation ◽  
Betula Platyphylla ◽  
Genome Survey ◽  
Third Generation Sequencing ◽  
Ssr Loci ◽  
Generation Sequencing

Research Highlights: A rigorous genome survey helped us to estimate the genomic characteristics, remove the DNA contamination, and determine the sequencing scheme of Betula platyphylla. Background and Objectives: B. platyphylla is a common tree species in northern China that has high economic and medicinal value. However, there is a lack of complete genomic information for this species, which severely constrains the progress of relevant research. The objective of this study was to survey the genome of B. platyphylla and determine the large-scale sequencing scheme of this species. Materials and Methods: Next-generation sequencing was used to survey the genome. The genome size, heterozygosity rate, and repetitive sequences were estimated by k-mer analysis. After preliminary genome assembly, sequence contamination was identified and filtered by sequence alignment. Finally, we obtained sterilized plantlets of B. platyphylla by plant tissue culture, which can be used for third-generation sequencing. Results: We estimated the genome size to be 432.9 Mb and the heterozygosity rate to be 1.22%, with repetitive sequences accounting for 62.2%. Bacterial contamination was observed in the leaves taken from the field, and most of the contaminants may be from the genus Mycobacterium. A total of 249,784 simple sequence repeat (SSR) loci were also identified in the B. platyphylla genome. Among the SSRs, only 11,326 can be used as candidates to distinguish the three Betula species. Conclusions: The B. platyphylla genome is complex and highly heterozygous and repetitive. Higher-depth third-generation sequencing may yield better assembly results. Sterilized plantlets can be used for sequencing to avoid contamination.

scholarly journals A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jihua Wang ◽  
Shiqiang Xu ◽  
Yu Mei ◽  
Shike Cai ◽  
Yan Gu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Assembly ◽  
Large Scale ◽  
Active Component ◽  
Southern China ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Comparative Genomic ◽  
Edible Plant ◽  
High Quality

AbstractMorinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.

scholarly journals Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 833-838 ◽  
Author(s):  
Scott A Jackson ◽  
Zhukuan Cheng ◽  
Ming Li Wang ◽  
Howard M Goodman ◽  
Jiming Jiang
Keyword(s):  
Arabidopsis Thaliana ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Brassica Rapa ◽  
Physical Mapping ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Comparative Genome ◽  
Artificial Chromosomes

Abstract Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

scholarly journals Population genetics of tandem repeats in centromeric heterochromatin: unequal crossing over and chromosomal divergence at the Responder locus of Drosophila melanogaster.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 477-487 ◽  
Author(s):  
E L Cabot ◽  
P Doshi ◽  
M L Wu ◽  
C I Wu
Keyword(s):  
Drosophila Melanogaster ◽  
Large Scale ◽  
Tandem Repeats ◽  
Evolutionary Dynamics ◽  
Repetitive Sequences ◽  
High Rate ◽  
Centromeric Heterochromatin ◽  
Crossing Over ◽  
Unequal Crossing Over ◽  
Left And Right

Abstract The Responder (Rsp) locus in Drosophila melanogaster is the target locus of segregation distortion and is known to be comprised of a tandem array of 120-bp repetitive sequences. In this study, we first determined the large scale molecular structure of the Rsp locus, which extends over a region of 600 kb on the standard sensitive (cn bw) chromosome. Within the region, small Rsp repeat arrays are interspersed with non-Rsp sequences and account for 10-20% of the total sequences. We isolated and sequenced 32 Rsp clones from three different chromosomes. The main results are: (1) Rsp repeats isolated from the same chromosome are not more similar than those from different chromosomes. This implies either that there are more homologous exchanges at the Rsp locus than expected or, alternatively, that the second chromosomes of D. melanogaster have diverged from one another more recently at the centromeric heterochromatin than at the nearby euchromatin. (2) The repeats usually have a dimeric structure with an average difference of 16% between the left and right halves. The differences allow us to easily identify the products of unequal exchanges. Despite the large differences between the two halves, exchanges have occurred frequently and the majority of them fall within a 29-bp interval of identity between the two halves. Our data thus support the suggestion that recombination depends on short stretches of complete identity rather than long stretches of general homology. (3) Frequent unequal crossover events obscure the phylogenetic relationships between repeats; therefore, different parts of any single repeat could often have different phylogenetic histories. The high rate of unequal crossing over may also help explain the evolutionary dynamics of the Rsp locus.

scholarly journals Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

2020 ◽  
Author(s):  
Mariela Sader ◽  
Magdalena Vaio ◽  
Luiz Augusto Cauz-Santos ◽  
Marcelo Carnier Dornelas ◽  
Maria Lucia Carneiro Vieira ◽  
...  
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Size Variation ◽  
Repetitive Dna Sequences ◽  
Ltr Retrotransposons ◽  
Genome Size Variation ◽  
Satellite Dnas

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

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