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Objective <p>Repetitive DNA comprises the majority of nuclear genomes in eukaryotes and is critical for genome stability, gene regulation and evolutionary innovation. Yet, most genomic surveys focus on lowcopy regions, leaving repeats underexplored. Here, we assess how repetitive elements shape genomic diversity and rapid radiation in <i>Dyckia</i> (Bromeliaceae) by characterizing the abundance, composition and variability of major repeat families using lowcoverage whole-genome sequencing and the RepeatExplorer2 pipeline.</p> Results description <p>A substantial proportion of <i>Dyckia</i> genome consists of repetitive DNA, reaching ~ 71% in <i>D. densiflora</i>, <i>D. elata</i>, and <i>D. consimilis</i>. Notable interspecific and intraspecific variation was observed, with <i>D. consimilis</i> ranging from 50.3 to 69.1%. Satellite DNA, though present in all species, varied in abundance (0.1–4.7%), indicating heterochromatin flexibility. Ty3/Gypsy and Ty1/Copia LTR retrotransposons dominate the repeatome, with lineage-specific expansions of Tekay and Ogre elements. Despite general conservation, population-level differences in repeat composition suggest a role in genome restructuring and phenotypic plasticity. These patterns point to repeat dynamics as a key driver of genome evolution, taxonomic complexity, and ecological adaptability in <i>Dyckia</i>.</p>

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Genomic characterization of repetitive DNA and transposable elements in Dyckia (Pitcairnioideae) species

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月9日

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  • João Victor da Silva Rabelo-Araujo,
  • Ana Flávia Francisconi,
  • Zirlane Portugal da Costa,
  • Caroline Bertocco Garcia,
  • Otavio Batista de Castro Ribeiro,
  • Ana Cristina Silva Amoroso Anastacio,
  • Maria Imaculada Zucchi

摘要

Objective

Repetitive DNA comprises the majority of nuclear genomes in eukaryotes and is critical for genome stability, gene regulation and evolutionary innovation. Yet, most genomic surveys focus on lowcopy regions, leaving repeats underexplored. Here, we assess how repetitive elements shape genomic diversity and rapid radiation in Dyckia (Bromeliaceae) by characterizing the abundance, composition and variability of major repeat families using lowcoverage whole-genome sequencing and the RepeatExplorer2 pipeline.

Results description

A substantial proportion of Dyckia genome consists of repetitive DNA, reaching ~ 71% in D. densiflora, D. elata, and D. consimilis. Notable interspecific and intraspecific variation was observed, with D. consimilis ranging from 50.3 to 69.1%. Satellite DNA, though present in all species, varied in abundance (0.1–4.7%), indicating heterochromatin flexibility. Ty3/Gypsy and Ty1/Copia LTR retrotransposons dominate the repeatome, with lineage-specific expansions of Tekay and Ogre elements. Despite general conservation, population-level differences in repeat composition suggest a role in genome restructuring and phenotypic plasticity. These patterns point to repeat dynamics as a key driver of genome evolution, taxonomic complexity, and ecological adaptability in Dyckia.