Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
    • Publication Information:
      Publication: London, UK : BioMed Central Ltd
      Original Publication: London : Genome Biology Ltd., c2000-
    • Subject Terms:
      Genome, Plant* ; Hybridization, Genetic*; Prunus/*genetics; Flowers/genetics ; Fruit/genetics ; Gene Expression ; Genes, Plant ; Genomics ; Haplotypes ; Prunus/metabolism ; Sequence Analysis, DNA ; Sympatry
    • Abstract:
      Background: Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology.
      Results: We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm.
      Conclusions: We report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.
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    • Grant Information:
      KNA1-1-13, 14-1 International Korea National Arboretum; PJ013194 International Rural Development Administration
    • Contributed Indexing:
      Keywords: Flowering Prunus; Hybrid genome; Long-read sequencing; S-locus haplotype; Sequence phase
    • Publication Date:
      Date Created: 20180906 Date Completed: 20190123 Latest Revision: 20230928
    • Publication Date:
      20231215
    • Accession Number:
      PMC6124018
    • Accession Number:
      10.1186/s13059-018-1497-y
    • Accession Number:
      30180884