Structural organization of the genome of the zygomycete Absidia glauca: evidence for high repetitive DNA content

1986 ◽  
Vol 10 (12) ◽  
pp. 903-907 ◽  
Author(s):  
Johannes W�stemeyer ◽  
Anke Burmester
Keyword(s):  
Repetitive Dna ◽  
Dna Content ◽  
Structural Organization ◽  
Absidia Glauca

Low repetitive DNA content in Aspergillus nidulans

Science ◽  
1978 ◽  
Vol 202 (4371) ◽  
pp. 973-975 ◽  
Author(s):  
W. Timberlake
Keyword(s):  
Aspergillus Nidulans ◽  
Repetitive Dna ◽  
Dna Content

Repetitive DNA in ThreeGramineaeSpecies with Low DNA Content

1980 ◽  
Vol 361 (2) ◽  
pp. 1223-1234 ◽  
Author(s):  
Vidya G. DESHPANDE ◽  
Prabhakar K. RANJEKAR
Keyword(s):  
Repetitive Dna ◽  
Dna Content

scholarly journals Tissue homogeneity requires inhibition of unequal gene silencing during development

2016 ◽  
Vol 214 (3) ◽  
pp. 319-331 ◽  
Author(s):  
Hai H. Le ◽  
Monika Looney ◽  
Benjamin Strauss ◽  
Michael Bloodgood ◽  
Antony M. Jose
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Gene Silencing ◽  
Repetitive Dna ◽  
Dna Content ◽  
Intestinal Cells ◽  
Cellular Processes ◽  
Cell Divisions ◽  
Developmental Mechanisms ◽  
Multicellular Organisms

Multicellular organisms can generate and maintain homogenous populations of cells that make up individual tissues. However, cellular processes that can disrupt homogeneity and how organisms overcome such disruption are unknown. We found that ∼100-fold differences in expression from a repetitive DNA transgene can occur between intestinal cells in Caenorhabditis elegans. These differences are caused by gene silencing in some cells and are actively suppressed by parental and zygotic factors such as the conserved exonuclease ERI-1. If unsuppressed, silencing can spread between some cells in embryos but can be repeat specific and independent of other homologous loci within each cell. Silencing can persist through DNA replication and nuclear divisions, disrupting uniform gene expression in developed animals. Analysis at single-cell resolution suggests that differences between cells arise during early cell divisions upon unequal segregation of an initiator of silencing. Our results suggest that organisms with high repetitive DNA content, which include humans, could use similar developmental mechanisms to achieve and maintain tissue homogeneity.

Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust

Chromosoma ◽  
2017 ◽  
Vol 127 (1) ◽  
pp. 45-57 ◽  
Author(s):  
Francisco J. Ruiz-Ruano ◽  
Josefa Cabrero ◽  
María Dolores López-León ◽  
Antonio Sánchez ◽  
Juan Pedro M. Camacho
Keyword(s):  
Repetitive Dna ◽  
Dna Content ◽  
Supernumerary Chromosome ◽  
Migratory Locust ◽  
Sequence Characterization

scholarly journals Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

2014 ◽  
Author(s):  
Maria Avila-Arcos ◽  
Marcela Sandoval-Velasco ◽  
Hannes Schroeder ◽  
Meredith L Carpenter ◽  
Anna-Sapfo Malaspinas ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Repetitive Dna ◽  
Ancient Dna ◽  
Dna Content ◽  
Important Influence ◽  
Whole Genome ◽  
Comparative Performance ◽  
Gc Composition

1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing. 2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments. 3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries. 4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.

scholarly journals Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Sixin Liu ◽  
Guangtu Gao ◽  
Ryan M. Layer ◽  
Gary H. Thorgaard ◽  
Gregory D. Wiens ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Repetitive Dna ◽  
Dna Content ◽  
Repetitive Sequences ◽  
Principal Component ◽  
Whole Genome ◽  
Structural Variants ◽  
High Confidence ◽  
Breeding Populations ◽  
Or Gene

Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies.

Repetitive DNA and chromosome evolution in plants

1986 ◽  
Vol 312 (1154) ◽  
pp. 227-242 ◽  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Dna Content ◽  
Molecular Mechanisms ◽  
Chromosome Structure ◽  
Species Turnover ◽  
Inverted Terminal Repeat ◽  
Repeated Dna ◽  
Higher Plant

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila , man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.

scholarly journals Blm Helicase Facilitates Rapid Replication of Repetitive DNA Sequences in early Drosophila Development

2021 ◽  
Author(s):  
Jolee M Ruchert ◽  
Morgan M Brady ◽  
Susan McMahan ◽  
Karly J Lacey ◽  
Leigh C. Latta ◽  
...  
Keyword(s):  
Dna Repair ◽  
Embryonic Development ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Dna Content ◽  
Replication Fork ◽  
Replication Stress ◽  
Sex Bias ◽  
Repetitive Dna Sequences ◽  
Cell Cycles

The absence of functional BLM DNA helicase, a member of the RecQ family of helicases, is responsible for the rare human disorder Bloom Syndrome, which results in developmental abnormalities, DNA repair defects, genomic instability, and a predisposition to cancer. In Drosophila melanogaster, the orthologous Blm protein is essential during early development when the embryo is under the control of maternal gene products. A lack of functional maternal Blm during the syncytial cell cycles of Drosophila embryonic development results in severe nuclear defects and lethality. Amongst the small fraction of embryos from Blm mutant mothers that survive to adulthood, a prominent sex-bias favors the class of flies that inherits less repetitive DNA content, which serves as an endogenous source of replication stress. This selection against repetitive DNA content reflects a role for Blm in facilitating replication through repetitive sequences during the rapid S-phases of syncytial cell cycles. During these syncytial cycles, Blm is not required for complex DNA repair; however, the progeny sex-bias resulting from the absence of maternal Blm is exacerbated by repetitive DNA sequences and by the slowing of replication fork progression, suggesting that the essential role for Blm during this stage is to manage replication fork stress brought about by impediments to fork progression. Additionally, our data suggest that Blm is only required to manage this replication stress during embryonic development, and likely only during the early, rapid syncytial cell cycles, and not at later developmental stages. These results provide novel insights into Blm function throughout development.

Integrative transformation of a zygomycete, Absidia glauca, with vectors containing repetitive DNA

1990 ◽  
Vol 17 (2) ◽  
pp. 155-161 ◽  
Author(s):  
Anke Burmester ◽  
Anke W�stemeyer ◽  
Johannes W�stemeyer
Keyword(s):  
Repetitive Dna ◽  
Absidia Glauca ◽  
Integrative Transformation
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