ArticleGenome biology2024
Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Toward a model of repeat-driven chromosomal fragility in Triticeae: an integrated structural omics perspective.BMC genomics · 2026Review
- Centromere evolution in annual and perennial soybeans and its implication for hybridization in cultivated species.Genome biology · 2026Article
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- The near-complete genome assembly of allotetraploidHorticulture research · 2026Article
- Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat.Genome research · 2025Article
- Pan-centromere landscape and dynamic evolution in Brassica plants.Nature plants · 2025Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
- Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.Genome biology · 2025Article
- The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.BMC biology · 2025Article
- Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae.Genome biology · 2025Article
- Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton.PLoS genetics · 2025Article
- A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites.Genome biology · 2025Article
- The gap-free genome ofHorticulture research · 2024Article
- Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus.Genome biology · 2024Article
- The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood.GigaScience · 2024Article
- Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis inFrontiers in plant science · 2024Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundCentromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different species in allopolyploids over millions of years remains largely unknown.
resultsHere, we generate three near-complete genome assemblies, a tetraploid Brachypodium hybridum and its two diploid ancestors, Brachypodium distachyon and Brachypodium stacei. We detect high degrees of sequence, structural, and epigenetic variations of centromeres at base-pair resolution between closely related Brachypodium genomes, indicating the appearance and accumulation of species-specific centromere repeats from a common origin during evolution. We also find that centromere homogenization is accompanied by local satellite repeats bursting and retrotransposon purging, and the frequency of retrotransposon invasions drives the degree of interspecies centromere diversification. We further investigate the dynamics of centromeres during alloploidization process, and find that dramatic genetics and epigenetics architecture variations are associated with the turnover of centromeres between homologous chromosomal pairs from diploid to tetraploid. Additionally, our pangenomes analysis reveals the ongoing variations of satellite repeats and stable evolutionary homeostasis within centromeres among individuals of each Brachypodium genome with different polyploidy levels.
conclusionsOur results provide unprecedented information on the genomic, epigenomic, and functional diversity of highly repetitive DNA between closely related species and their allopolyploid genomes at both coarse and fine scale.
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