ArticlePloS one2019
The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages.
Article in PloS one, 2019. 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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8 citing papers in PubMed, 12 citations in OpenAlex.
- Exploring Genetic Diversity and Inter-/Intraspecific Polymorphism inInternational journal of molecular sciences · 2025Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genusFrontiers in plant science · 2024Article
- Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements in Barley (Frontiers in plant science · 2024Article
- Gene structure and potential regulation of the lycopene cyclase genes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure ofInternational journal of molecular sciences · 2023Article
- Regulatory mechanisms behind the phenotypic plasticity associated with Setaria italica water deficit tolerance.Plant molecular biology · 2022Article
- Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate.Nature communications · 2020Article
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5 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Long terminal repeat retrotransposons (LTR-RTs) in plant genomes differ in abundance, structure and genomic distribution, reflecting the large number of evolutionary lineages. Elements within lineages can be considered populations, in which each element is an individual in its genomic environment. In this way, it would be reasonable to apply microevolutionary analyses to understand transposable element (TE) evolution, such as those used to study the genetic structure of natural populations. Here, we applied a Bayesian method to infer genetic structure of populations together with classical phylogenetic and dating tools to analyze LTR-RT evolution using the monocot Setaria italica as a model species. In contrast to a phylogeny, the Bayesian clusterization method identifies populations by assigning individuals to one or more clusters according to the most probabilistic scenario of admixture, based on genetic diversity patterns. In this work, each LTR-RT insertion was considered to be one individual and each LTR-RT lineage was considered to be a single species. Nine evolutionary lineages of LTR-RTs were identified in the S. italica genome that had different genetic structures with variable numbers of clusters and levels of admixture. Comprehensive analysis of the phylogenetic, clusterization and time of insertion data allowed us to hypothesize that admixed elements represent sequences that harbor ancestral polymorphic sequence signatures. In conclusion, application of microevolutionary concepts in genome evolution studies is suitable as a complementary approach to phylogenetic analyses to address the evolutionary history and functional features of TEs.
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