ArticlePloS one2011
Next generation sequencing-based analysis of repetitive DNA in the model dioecious [corrected] plant Silene latifolia.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
- Post-polyploidization centromere evolution in cotton.Nature genetics · 2025Article
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- Telomeres and Their Neighbors.Genes · 2022Review
- Identification of 45S rDNA in Passiflora using low coverage sequencing: analysis of GC content and chromosomal localization.Molecular biology reports · 2022Article
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- The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass,Frontiers in plant science · 2022Article
- Chromosome and Genome Diversity in the GenusPlants (Basel, Switzerland) · 2021Review
- Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome.Planta · 2021Article
- The Genomics of Plant Satellite DNA.Progress in molecular and subcellular biology · 2021Review
- Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the GenusFrontiers in genetics · 2021Article
- Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae).Frontiers in plant science · 2021Article
- Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses.BMC plant biology · 2020Article
- Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
- Characterization and Dynamics of Repeatomes in Closely Related Species ofFrontiers in plant science · 2020Article
- Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis inFrontiers in plant science · 2020Article
- TheFrontiers in genetics · 2020Article
- Fluorescence in situ hybridization in plants: recent developments and future applications.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2019Review
- Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA.BMC genomics · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSilene latifolia is a dioecious [corrected] plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. METHODOLOGY/PRINCIPAL
findingsWe performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. CONCLUSIONS/SIGNIFICANCE: This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome.
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