Structural and functional liaisons between transposable elements and satellite DNAs

Meštrović, Nevenka; Mravinac, Brankica; Pavlek, Martina; Vojvoda-Zeljko, Tanja; Šatović, Eva; Plohl, Miroslav

doi:10.1007/s10577-015-9483-7

Cited by 112 publications

(120 citation statements)

References 103 publications

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“…No other satDNA carrying microsatellites was found. Taken together, these results suggest the possibility that some satDNAs in L. migratoria originated from TEs, as in other organisms1718.…”

Section: Resultsmentioning

confidence: 57%

High-throughput analysis of the satellitome illuminates satellite DNA evolution

Ruiz‐Ruano

López-León

Cabrero

et al. 2016

Sci Rep

198

307

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Satellite DNA (satDNA) is a major component yet the great unknown of eukaryote genomes and clearly underrepresented in genome sequencing projects. Here we show the high-throughput analysis of satellite DNA content in the migratory locust by means of the bioinformatic analysis of Illumina reads with the RepeatExplorer and RepeatMasker programs. This unveiled 62 satDNA families and we propose the term “satellitome” for the whole collection of different satDNA families in a genome. The finding that satDNAs were present in many contigs of the migratory locust draft genome indicates that they show many genomic locations invisible by fluorescent in situ hybridization (FISH). The cytological pattern of five satellites showing common descent (belonging to the SF3 superfamily) suggests that non-clustered satDNAs can become into clustered through local amplification at any of the many genomic loci resulting from previous dissemination of short satDNA arrays. The fact that all kinds of satDNA (micro- mini- and satellites) can show the non-clustered and clustered states suggests that all these elements are mostly similar, except for repeat length. Finally, the presence of VNTRs in bacteria, showing similar properties to non-clustered satDNAs in eukaryotes, suggests that this kind of tandem repeats show common properties in all living beings.

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Section: Resultsmentioning

confidence: 57%

High-throughput analysis of the satellitome illuminates satellite DNA evolution

Ruiz‐Ruano

López-León

Cabrero

et al. 2016

Sci Rep

198

307

View full text Add to dashboard Cite

show abstract

“…For example, analysis in five complete plant genomes showed that microsatellites were preferentially located in unique regions of the genomes and exhibited a lack of association with transposon-rich regions 38 . It was hypothesized that microsatellite can be derived from TEs and the opposite evolutionary direction may occur 50, 51 . The direction of transition from TE to microsatellite might depend on transposition rate with an optimal value and the opposite transition is linked to recombination rate 50, 51 .…”

Section: Discussionmentioning

confidence: 99%

“…It was hypothesized that microsatellite can be derived from TEs and the opposite evolutionary direction may occur 50, 51 . The direction of transition from TE to microsatellite might depend on transposition rate with an optimal value and the opposite transition is linked to recombination rate 50, 51 . A chromosome-biased association between microsatellites and TEs in our study is presumably at least partially related to their distant contact and recombination behavior of chromosomes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Chen

Huang

et al. 2017

Sci Rep

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We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.

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“…A body of non‐avian evidence suggests direct involvement of TEs in shaping centromere architecture (reviewed in Refs. and ), and we note that centromeric TEs can thereby affect speciation through the meiotic process of centromere drive (reviewed in Refs. and ).…”

Section: Third‐generation Genome Assemblies and The Future Of Avian Gmentioning

confidence: 96%

Evolution of bird genomes—a transposon's‐eye view

Kapusta

Suh

2016

Annals of the New York Academy of Sciences

141

158

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Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

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Structural and functional liaisons between transposable elements and satellite DNAs

Cited by 112 publications

References 103 publications

High-throughput analysis of the satellitome illuminates satellite DNA evolution

High-throughput analysis of the satellitome illuminates satellite DNA evolution

Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Evolution of bird genomes—a transposon's‐eye view

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