ArticleBMC genomics2024
Karyotype and LTR-RTs analysis provide insights into oak genomic evolution.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 7 citations in OpenAlex.
- Expression dynamics of starch and proanthocyanidin biosynthesis genes during Quercus glauca fruit development.BMC plant biology · 2026Article
- Chromosome-Level Genome Assembly and Comparative Genomic Analysis ofPlants (Basel, Switzerland) · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
- Role of chromosome ends in meiotic stability, recombination and wheat evolution in the context of breeding.BMC plant biology · 2025Article
- Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis.Plants (Basel, Switzerland) · 2025Article
- Optimization of Chromosome Preparation and Karyotype Analysis of Winter Turnip Rape (International journal of molecular sciences · 2025Article
- Response of Pedunculate Oak (Plants (Basel, Switzerland) · 2025Review
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundWhole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.
resultsKaryotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.
conclusionChromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
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