ArticleSystematic biology2015
Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.
Article in Systematic biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.The plant genome · 2026Article
- The afterlife of a horizontally transferred gene: Expansion and functional diversification of a C1A peptidase in wild Hordeum species.The plant genome · 2026Article
- Species of the Genus ×Plants (Basel, Switzerland) · 2026Article
- Phylogenomic conflict inPlant diversity · 2026Article
- A chromosome-scale genome assembly of Hordeum erectifolium: genomic, transcriptomic and anatomical adaptations to drought in a wild barley relative.The New phytologist · 2026Article
- Integrative analysis of plastome, single-copy nuclear genePlant diversity · 2026Article
- Climate change reshapes the global distribution of wild barley relatives: integrating life-history traits and ecological niche modeling.Frontiers in plant science · 2026Article
- Pan-chloroplast genomes ofFrontiers in plant science · 2026Article
- Genomic Composition of the Artificial Hybrid ×Plants (Basel, Switzerland) · 2025Article
- Robust regression rescues poor phylogenetic decisions.BMC ecology and evolution · 2025Article
- Phylogenomics of Western Eurasian Tilia: merging GBS datasets to place the Hyrcanian forest limes.BMC plant biology · 2025Article
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- Marker-trait association analysis for root and shoot traits at the seedling stage of wild barley (AoB PLANTS · 2025Article
- Participation of Wild Species GenusPlants (Basel, Switzerland) · 2025Article
- Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement.Nature plants · 2025Article
- A Hordeum I-genome sequence provides insight into how plants adapt to salt-alkali stress.Nature plants · 2025Article
- Phylogeny and taxonomy of the polyploid species that contain St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes.BMC plant biology · 2025Article
- Article
- Genetic Diversity of the Species of the GenusInternational journal of molecular sciences · 2024Article
- Plant pangenomes for crop improvement, biodiversity and evolution.Nature reviews. Genetics · 2024Review
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2 authors.
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Abstract
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.
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