ArticleSystematic biology2015
Genomic repeat abundances contain phylogenetic signal.
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81 citing papers in PubMed.
- Dynamic evolution and hierarchical regulation of rDNA in polyploid oat.The Plant journal : for cell and molecular biology · 2026Article
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- The complete chloroplast genome sequence of Typhonium flagelliforme, an anti-cancer medicinal plant: genome structure, comparative and phylogenetic relationship analysis within Araceae.Functional & integrative genomics · 2026Article
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- The repeatome landscape in the "Frontiers in plant science · 2026Article
- Complete chloroplast genome ofFrontiers in plant science · 2026Article
- A comparative analysis of transposable element diversity and evolution across 75 bee genomes.BMC genomics · 2025Article
- 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
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- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication.Annals of botany · 2025Article
- The first insight into Acanthocephalus (Palaeacanthocephala) satellitome: species-specific satellites as potential cytogenetic markers.Scientific reports · 2025Article
- Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes.Genome biology and evolution · 2025Article
- Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification.Frontiers in plant science · 2025Article
- How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics.Frontiers in plant science · 2025Article
- Holocentric repeat landscapes: From micro-evolutionary patterns to macro-evolutionary associations with karyotype evolution.Molecular ecology · 2024Article
- Complete Chloroplast Genome ofGenes · 2024Article
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- Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis inFrontiers in plant science · 2024Article
21 more citing papers are in PubMed but not listed here.
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9 authors.
Steven DodsworthSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Mark W ChaseSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Laura J KellySchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Ilia J LeitchSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Jiří MacasSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Petr NovákSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Mathieu PiednoëlSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Hanna Weiss-SchneeweissSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
Andrew R LeitchSchool of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria a.r.leitch@qmul.ac.uk.
Funding
Austrian Science Fund FWF P 21440
Abstract
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
Indexed as
PhylogenyAnimalsCluster AnalysisDNA, PlantDrosophilaGenes, InsectGenomeMagnoliopsidaRepetitive Sequences, Nucleic AcidDNA, Plantcontinuous charactersgenomicsmolecular systematicsnext-generation sequencingphylogeneticsRepetitive DNA
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