scholarly journals Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

2019 ◽  
Vol 101 (2) ◽  
pp. 484-500 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats

Isolation and characterization of tandem repeats in nematode genomes.

2021 ◽  
pp. 240-249
Author(s):  
Philippe Castagnone-Sereno
Keyword(s):  
Case Studies ◽  
Genetic Markers ◽  
Satellite Dna ◽  
Entomopathogenic Nematodes ◽  
Tandem Repeats ◽  
Genomic Resources ◽  
Isolation And Characterization ◽  
Nematode Genomes ◽  
Plant Parasitic

Abstract This chapter provides an overview of the practical methodologies that can be used to identify and characterize the tandem repeats that are most frequently used as genetic markers in nematodes (including plant-parasitic and entomopathogenic nematodes), namely satellite DNA and microsatellites. The objective is not to provide turnkey protocols, but rather to return to the main principles that govern these protocols. Case studies on nematodes will serve to illustrate the point. In that respect, two well-defined situations are to be considered, depending on whether genomic resources for the species under investigation are available or not.

scholarly journals Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

2019 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Length Distribution ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Satellite Repeat ◽  
Major Satellite ◽  
Satellite Repeats ◽  
Genome Wide

AbstractBackgroundAmplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities.ResultsWe have developed a computational workflow for similarity-based detection and downstream analysis of satellite repeats in individual nanopore reads that led to genome-wide characterization of their properties. Using the satellite DNA-rich legume plantLathyrus sativusas a model, we demonstrated this approach by analyzing eleven major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of theL. sativuschromosomes, which suggests that these genome regions are favorable for satellite DNA accumulation.ConclusionsThe presented approach proved to be efficient in revealing differences in long-range organization of satellite repeats that can be used to investigate their origin and evolution in the genome.

Isolation and characterization of tandem repeats in nematode genomes.

2021 ◽  
pp. 240-249
Author(s):  
Philippe Castagnone-Sereno
Keyword(s):  
Case Studies ◽  
Genetic Markers ◽  
Satellite Dna ◽  
Entomopathogenic Nematodes ◽  
Tandem Repeats ◽  
Genomic Resources ◽  
Isolation And Characterization ◽  
Nematode Genomes ◽  
Plant Parasitic

Abstract This chapter provides an overview of the practical methodologies that can be used to identify and characterize the tandem repeats that are most frequently used as genetic markers in nematodes (including plant-parasitic and entomopathogenic nematodes), namely satellite DNA and microsatellites. The objective is not to provide turnkey protocols, but rather to return to the main principles that govern these protocols. Case studies on nematodes will serve to illustrate the point. In that respect, two well-defined situations are to be considered, depending on whether genomic resources for the species under investigation are available or not.

scholarly journals Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

2021 ◽  
Vol 22 (9) ◽  
pp. 4707
Author(s):  
Mariana Lopes ◽  
Sandra Louzada ◽  
Margarida Gama-Carvalho ◽  
Raquel Chaves
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Nucleotide Composition ◽  
Genomic Component ◽  
Genomic Studies ◽  
Human Genomic ◽  
Definition Of ◽  
High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

scholarly journals Characterization of the Genomic Xist Locus in Rodents Reveals Conservation of Overall Gene Structure and Tandem Repeats but Rapid Evolution of Unique Sequence

2001 ◽  
Vol 11 (5) ◽  
pp. 833-849 ◽  
Author(s):  
T. B. Nesterova ◽  
S. Ya. Slobodyanyuk ◽  
E. A. Elisaphenko ◽  
A. I. Shevchenko ◽  
C. Johnston ◽  
...  
Keyword(s):  
Gene Structure ◽  
Tandem Repeats ◽  
Rapid Evolution ◽  
Unique Sequence ◽  
Xist Locus

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

The Drosophila pumilio gene: an unusually long transcription unit and an unusual protein

Development ◽  
1992 ◽  
Vol 114 (1) ◽  
pp. 221-232 ◽  
Author(s):  
P.M. Macdonald
Keyword(s):  
Amino Acid ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Transcription Unit ◽  
Posterior Pole ◽  
Single Amino Acid ◽  
Cdna Sequences ◽  
Subcortical Region ◽  
Mrna And Protein Expression

Specification of the posterior body plan in Drosophila requires the action of a determinant prelocalized to the posterior pole of the embryo. During embryogenesis this determinant appears to move anteriorly in a process dependent on the pumilio (pum) gene. This report describes the cloning and molecular characterization of a cDNA derived from the pum gene, and the analysis of pum mRNA and protein expression during early Drosophila development. The pum gene is unusually large; comparison of genomic and cDNA sequences reveals that the pum transcription unit is at least 160 kb in length. The pum cDNA encodes a 157 × 10(3) M(r) protein which consists mainly of regions enriched in a single amino acid, usually glycine, alanine, glutamine or serine/threonine. Six tandem repeats of a 36 amino acid repeat unit are also present. Pum protein is cytoplasmic and is concentrated in a subcortical region of the embryo. The distribution of pum protein exhibits no asymmetry along the anteroposterior axis of the embryo.

scholarly journals Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 352 ◽  
Author(s):  
Karen H. Miga
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Human Population ◽  
Sequence Variation ◽  
Tandem Repeats ◽  
Association Studies ◽  
Unmet Need ◽  
Satellite Dnas ◽  
Dna Variation ◽  
Medical Genomics

The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional association studies currently ignore millions of bases that span each centromeric region and acrocentric short arm. These regions are enriched in long arrays of tandem repeats, or satellite DNAs, that are known to vary extensively in copy number and repeat structure in the human population. Satellite sequence variation in the human genome is often so large that it is detected cytogenetically, yet due to the lack of a reference assembly and informatics tools to measure this variability, contemporary high-resolution disease association studies are unable to detect causal variants in these regions. Nevertheless, recently uncovered associations between satellite DNA variation and human disease support that these regions present a substantial and biologically important fraction of human sequence variation. Therefore, there is a pressing and unmet need to detect and incorporate this uncharacterized sequence variation into broad studies of human evolution and medical genomics. Here I discuss the current knowledge of satellite DNA variation in the human genome, focusing on centromeric satellites and their potential implications for disease.

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