An 82 bp tandem repeat family typical of 3' non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres

Genome ◽  
2021 ◽  
Author(s):  
Leonardo Adabo Cintra ◽  
Thaissa Boldieri de Souza ◽  
Letícia Maria Parteka ◽  
Lucas Mesquita Barreto ◽  
Luiz Filipe Protasio Pereira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Tandem Repeat ◽  
Dna Sequences ◽  
Ltr Retrotransposons ◽  
Non Coding Rna ◽  
Functional Aspects ◽  
Good Coverage ◽  
Short Tandem

Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around centromeres. However, proximal regions of Coffea chromosomes remain poorly understood, especially on the nature and organisation of the sequences. Taking advantage of genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extend from pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improve our understanding of the role of Gypsy/TAT LTR retrotransposon lineage in the organization of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships with fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

scholarly journals Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Octavio M. Palacios-Gimenez ◽  
Julia Koelman ◽  
Marc Palmada-Flores ◽  
Tessa M. Bradford ◽  
Karl K. Jones ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Species Complex ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Large Genome ◽  
Chromosomal Races

Abstract Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

scholarly journals Transposable elements in natural populations of Drosophila melanogaster

2010 ◽  
Vol 365 (1544) ◽  
pp. 1219-1228 ◽  
Author(s):  
Yuh Chwen G. Lee ◽  
Charles H. Langley
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Copy Number ◽  
Population Genomics ◽  
Natural Populations ◽  
Crossing Over ◽  
Large Role ◽  
Essential Components ◽  
Replicative Transposition

Transposable elements (TEs) are families of small DNA sequences found in the genomes of virtually all organisms. The sequences typically encode essential components for the replicative transposition sequences of that TE family. Thus, TEs are simply genomic parasites that inflict detrimental mutations on the fitness of their hosts. Several models have been proposed for the containment of TE copy number in outbreeding host populations such as Drosophila . Surveys of the TEs in genomes from natural populations of Drosophila have played a central role in the investigation of TE dynamics. The early surveys indicated that a typical TE insertion is rare in a population, which has been interpreted as evidence that each TE is selected against. The proposed mechanisms of this natural selection are reviewed here. Subsequent and more targeted surveys identify heterogeneity among types of TEs and also highlight the large role of homologous and possibly ectopic crossing over in the dynamics of the Drosophila TEs. The recent discovery of germline-specific RNA interference via the piwi-interacting RNA pathway opens yet another interesting mechanism that may be critical in containing the copy number of TEs in natural populations of Drosophila . The expected flood of Drosophila population genomics is expected to rapidly advance understanding of the dynamics of TEs.

scholarly journals Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards

2016 ◽  
Vol 283 (1840) ◽  
pp. 20161555 ◽  
Author(s):  
Nathalie Feiner
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Adaptive Radiation ◽  
Genome Structure ◽  
Gene Clusters ◽  
Genomic Region ◽  
High Rate ◽  
Morphological Adaptations ◽  
Genomic Regions

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region ( Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis , TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.

scholarly journals Transposable Elements in the Genome of Human Parasite Schistosoma mansoni: A Review

2021 ◽  
Vol 6 (3) ◽  
pp. 126
Author(s):  
Gisele Strieder Philippsen
Keyword(s):  
Gene Duplication ◽  
Transposable Elements ◽  
Schistosoma Mansoni ◽  
Dna Sequences ◽  
Current Knowledge ◽  
Coding Sequences ◽  
Human Parasite ◽  
Relevant Role ◽  
Duplication Events

Transposable elements (TEs) are DNA sequences able to transpose within the host genome and, consequently, influence the dynamics of evolution in the species. Among the possible effects, TEs insertions may alter the expression and coding patterns of genes, leading to genomic innovations. Gene-duplication events, resulting from DNA segmental duplication induced by TEs transposition, constitute another important mechanism that contributes to the plasticity of genomes. This review aims to cover the current knowledge regarding TEs in the genome of the parasite Schistosoma mansoni, an agent of schistosomiasis—a neglected tropical disease affecting at least 250 million people worldwide. In this context, the literature concerning TEs description and TEs impact on the genomic architecture for S. mansoni was revisited, displaying evidence of TEs influence on schistosome speciation—mediated by bursts of transposition—and in gene-duplication events related to schistosome–host coevolution processes, as well several instances of TEs contribution into the coding sequences of genes. These findings indicate the relevant role of TEs in the evolution of the S. mansoni genome.

Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species

2020 ◽  
Vol 160 (9) ◽  
pp. 554-564
Author(s):  
Agus B. Setiawan ◽  
Chee H. Teo ◽  
Shinji Kikuchi ◽  
Hidenori Sassa ◽  
Kenji Kato ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Cucumis Melo ◽  
Repetitive Dna Sequences ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Mitotic Chromosomes ◽  
Rna Genes

Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that <i>Menolird18</i>, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in <i>Cucumis melo</i>, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, <i>Menolird18</i> was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of <i>Menolird18</i> were found in centromeric and rDNA regions of mitotic chromosomes suggests that <i>Menolird18</i> is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of <i>Menolird18</i> in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (<i>C. melo</i>) and cucumber (<i>C. sativus</i>) genomes.

scholarly journals Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes

2020 ◽  
Vol 12 (11) ◽  
pp. 1965-1974
Author(s):  
Hanhan Xia ◽  
Wei Zhao ◽  
Yong Shi ◽  
Xiao-Ru Wang ◽  
Baosheng Wang
Keyword(s):  
Tandem Repeat ◽  
Structural Variation ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Mitochondrial Genomes ◽  
Repeat Array ◽  
Mitochondrial Genome Evolution ◽  
Tandem Duplications ◽  
Short Tandem

Abstract Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

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