Chimeras Linked to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

2017 ◽  
Vol 19 (4) ◽  
pp. 401-409 ◽  
Author(s):  
Lihai Ye ◽  
Ni Jiao ◽  
Xiaojun Tang ◽  
Yiyi Chen ◽  
Xiaolan Ye ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Tetraploid Hybrid ◽  
Hybrid Fish

scholarly journals Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

2016 ◽  
Author(s):  
Lihai Ye ◽  
Xiaojun Tang ◽  
Yiyi Chen ◽  
Li Ren ◽  
Fangzhou Hu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Artificial Chromosome ◽  
Strand Break ◽  
Bacterial Artificial Chromosomes ◽  
Distant Hybridization ◽  
Artificial Chromosomes ◽  
Hybrid Fish ◽  
The Relationship ◽  
Allotetraploid Hybrid

AbstractThe formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.

scholarly journals Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline

2001 ◽  
Vol 11 (13) ◽  
pp. 1017-1027 ◽  
Author(s):  
Alexei A. Aravin ◽  
Natalia M. Naumova ◽  
Alexei V. Tulin ◽  
Vasilii V. Vagin ◽  
Yakov M. Rozovsky ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Double Stranded Rna

APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition

2007 ◽  
Vol 35 (3) ◽  
pp. 637-642 ◽  
Author(s):  
G.G. Schumann
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Genetic Disorders ◽  
Single Copy ◽  
Long Terminal Repeat Retrotransposons ◽  
Variable Number ◽  
Ltr Retrotransposons ◽  
Negative Effects ◽  
Processed Pseudogenes ◽  
Retrotransposon Activity

Mammalian genomes are littered with enormous numbers of transposable elements interspersed within and between single-copy endogenous genes. The only presently spreading class of human transposable elements comprises non-LTR (long terminal repeat) retrotransposons, which cover approx. 34% of the human genome. Non-LTR retrotransposons include the widespread autonomous LINEs (long interspersed nuclear elements) and non-autonomous elements such as processed pseudogenes, SVAs [named after SINE (short interspersed nuclear element), VNTR (variable number of tandem repeats) and Alu] and SINEs. Mobilization of these elements affects the host genome, can be deleterious to the host cell, and cause genetic disorders and cancer. In order to limit negative effects of retrotransposition, host genomes have adopted several strategies to curb the proliferation of transposable elements. Recent studies have demonstrated that members of the human APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) protein family inhibit the mobilization of the non-LTR retrotransposons LINE-1 and Alu significantly and participate in the intracellular defence against retrotransposition by mechanisms unknown to date. The striking coincidence between the expansion of the APOBEC3 gene cluster and the abrupt decline in retrotransposon activity in primates raises the possibility that these genes may have been expanded to prevent genomic instability caused by endogenous retroelements.

scholarly journals Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome

2010 ◽  
Vol 5 (1) ◽  
pp. 18 ◽  
Author(s):  
Shi Wang ◽  
Lingling Zhang ◽  
Eli Meyer ◽  
Zhenmin Bao
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
E. V. Evtushenko ◽  
V. G. Levitsky ◽  
E. A. Elisafenko ◽  
K. V. Gunbin ◽  
A. I. Belousov ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats

scholarly journals De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines

2019 ◽  
Author(s):  
Bráulio S.M.L. Silva ◽  
Pedro Heringer ◽  
Guilherme B. Dias ◽  
Marta Svartman ◽  
Gustavo C.S. Kuhn
Keyword(s):  
Transposable Elements ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
De Novo ◽  
Chromosome Mapping ◽  
Drosophila Virilis ◽  
Satellite Dnas ◽  
Bioinformatic Tools ◽  
A Genome ◽  
Genome Assemblies

AbstractSatellite DNAs are among the most abundant repetitive DNAs found in eukaryote genomes, where they participate in a variety of biological roles, from being components of important chromosome structures to gene regulation. Experimental methodologies used before the genomic era were not sufficient despite being too laborious and time-consuming to recover the collection of all satDNAs from a genome. Today, the availability of whole sequenced genomes combined with the development of specific bioinformatic tools are expected to foster the identification of virtually all of the “satellitome” from a particular species. While whole genome assemblies are important to obtain a global view of genome organization, most assemblies are incomplete and lack repetitive regions. Here, we applied short-read sequencing and similarity clustering in order to perform a de novo identification of the most abundant satellite families in two Drosophila species from the virilis group: Drosophila virilis and D. americana. These species were chosen because they have been used as a model to understand satDNA biology since early 70’s. We combined computational tandem repeat detection via similarity-based read clustering (implemented in Tandem Repeat Analyzer pipeline – “TAREAN”) with data from the literature and chromosome mapping to obtain an overview of satDNAs in D. virilis and D. americana. The fact that all of the abundant tandem repeats we detected were previously identified in the literature allowed us to evaluate the efficiency of TAREAN in correctly identifying true satDNAs. Our results indicate that raw sequencing reads can be efficiently used to detect satDNAs, but that abundant tandem repeats present in dispersed arrays or associated with transposable elements are frequent false positives. We demonstrate that TAREAN with its parent method RepeatExplorer, may be used as resources to detect tandem repeats associated with transposable elements and also to reveal families of dispersed tandem repeats.

scholarly journals The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing

2019 ◽  
Vol 124 (1) ◽  
pp. 103-120 ◽  
Author(s):  
Petra Hloušková ◽  
Terezie Mandáková ◽  
Milan Pouch ◽  
Pavel Trávníček ◽  
Martin A Lysak
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Tandem Repeats ◽  
Dna Repeats ◽  
Annual Life Cycle ◽  
Genome Size Variation ◽  
Genome Size Evolution ◽  
Nuclear Genomes

Abstract Background and Aims Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062–2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256–4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. Methods Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. Key Results Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. Conclusions The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.

Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats

2015 ◽  
Vol 24 ◽  
pp. 335-341 ◽  
Author(s):  
Manuel Vera ◽  
Xabier Bello ◽  
Jose-Antonio Álvarez-Dios ◽  
Belen G. Pardo ◽  
Laura Sánchez ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Ostrea Edulis ◽  
Flat Oyster ◽  
Short Tandem

scholarly journals Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Musaddeque Ahmed ◽  
Ping Liang
Keyword(s):  
Transposable Elements ◽  
Human Genome ◽  
Tandem Repeats ◽  
Sequence Similarity ◽  
Genomic Alteration ◽  
Repeat Elements ◽  
Significant Contributor ◽  
Repeat Units ◽  
Local Duplication ◽  
The Relationship

Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276 TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ∼0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats.

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