ArticleMolecular biology and evolution2022
IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 21 citations in OpenAlex.
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- Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.Nature communications · 2025Article
- Comparative genomics approach to infer ancestral cell karyotypes and reconstruct the evolutionary trajectories of plant chromosomes.Nature protocols · 2025Review
- The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.Cell genomics · 2024Article
- Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.Plant communications · 2024Article
- A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms.Plant communications · 2024Article
- Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae.BMC genomics · 2024Article
- Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.Nature genetics · 2024Article
- The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones.Plant communications · 2024Article
- A chromosome-level genome assembly for Onobrychis viciifolia reveals gene copy number gain underlying enhanced proanthocyanidin biosynthesis.Communications biology · 2024Article
- Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum.BMC biology · 2023Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Significant improvements in genome sequencing and assembly technology have led to increasing numbers of high-quality genomes, revealing complex evolutionary scenarios such as multiple whole-genome duplication events, which hinders ancestral genome reconstruction via the currently available computational frameworks. Here, we present the Inferring Ancestor Genome Structure (IAGS) framework, a novel block/endpoint matching optimization strategy with single-cut-or-join distance, to allow ancestral genome reconstruction under both simple (single-copy ancestor) and complex (multicopy ancestor) scenarios. We evaluated IAGS with two simulated data sets and applied it to four different real evolutionary scenarios to demonstrate its performance and general applicability. IAGS is available at https://github.com/xjtu-omics/IAGS.
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