ArticleThe Plant journal : for cell and molecular biology2020
Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats.
Article in The Plant journal : for cell and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 106 citations in OpenAlex.
- Reciprocal constraint couples architectural protein abundance and pericentromeric satellite expansion.bioRxiv : the preprint server for biology · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Evolutionary trends of As51 satellite DNA and its colocalization with 45S ribosomal DNA: a conserved feature in Characiformes fishes.BMC genomics · 2026Article
- TONSOKU prevents the formation of large tandem duplications and restrains ATR-WEE1 checkpoint activation.Nature communications · 2026Article
- Asymmetric evolution of satellite DNA on homologous and homeologous chromosomes in allotetraploid Narenga porphyrocoma.BMC plant biology · 2026Article
- The maize B chromosome shapes the transcriptome throughout the entire plant life cycle.Journal of experimental botany · 2025Article
- Satellite DNA Genomics: The Ongoing Story.International journal of molecular sciences · 2025Review
- From minor loci to major players? Satellite DNA diversification in Crepis sensu stricto.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Divergent landscapes and evolutionary trajectories of 5S rDNA and Cassandra retroelement in Saccharinae.BMC plant biology · 2025Article
- Satellite DNAs rising from the transposon graveyards.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Review
- Expansion of satellite DNAs derived from transposable elements in beetles with reduced diploid numbers.Heredity · 2025Article
- Taxonomy, Phylogeny, Genomes, and Repeatomes in the SubgeneraInternational journal of molecular sciences · 2025Review
- Retand LTR-retrotransposons in plants: a long way from pol to 3'LTR.Mobile DNA · 2025Article
- The highly dynamic satellitomes of cultivated wheat species.Annals of botany · 2024Article
- SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies.Briefings in bioinformatics · 2024Article
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- The genetic mechanism of B chromosome drive in rye illuminated by chromosome-scale assembly.Nature communications · 2024Article
- Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.Molecular biology and evolution · 2024Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplification 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. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73× 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 the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.