ArticleNature genetics2024
Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- Tandem duplication underlies diversification of the gymnosperm-specific TPS-d subfamily.Horticulture research · 2026Article
- Sarcandra glabra genome unveils functional conservation and divergence of O-methyltransferases catalyzing isofraxidin biosynthesis in angiosperms.Nature communications · 2026Article
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Integrative sequence-structure analysis reveals hidden WD40 domains forming stable β-propeller folds with potential biological functions in plants.Plant communications · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.Cell reports · 2026Article
- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance.The plant genome · 2026Article
- A Near-Telomere-to-Telomere Genome Assembly of the Spotted Seal (International journal of molecular sciences · 2026Article
- Population genetic structure reveals asymmetric hybridization between Pinus pumila and P. parviflora var. Pentaphylla in the Hakkoda Mountains, Northern Japan.Scientific reports · 2025Article
- Manipulating Unisexual-Sexual Reproduction Transition to Engineer Genome-Reconstructed Polyploids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A complex interplay of genetic introgression and local adaptation during the evolutionary history of three closely related spruce species.Plant diversity · 2025Article
- Ovule development and pollen tube growth in Tsuga chinensis: insights into the evolution of siphonogamy.Plant cell reports · 2025Article
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26 authors.
Funding
Abstract
Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence-absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora.
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