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

Seunghoon Baek,Ara Cho,Kyung Choi,Goon-Bo Kim,Hyuk-Jin Kim,Hee-Ju Yu,Jeong-Hwan Mun,Hoyeol Jang,Changkyun Kim,Joo-Hwan Kim,Kae Sun Chang

doi:10.1186/s13059-018-1497-y

Abstract

BackgroundHybridization 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.ResultsWe 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.ConclusionsWe 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.

Highlights

Hybridization is an important evolutionary process that results in increased plant diversity
With the aim of describing the hybrid genome, which is fundamental for understanding the structure and organization of the hybrid flowering Prunus genome, in this study, we report the draft genome assembly, annotation, and analysis of the heterozygous wild P. yedoensis (Pyn) genome based on PacBio RSII long-read sequencing refined with Illumina short-read sequences
Heterozygous genomic nature of wild P. yedoensis Pyn-Jeju2 is an endemic wild flowering cherry tree preserved in a natural habitat on Jeju Island, Korea with a

Summary

Introduction

Hybridization is an important evolutionary process that results in increased plant diversity. The genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. The sequencing and assembly of the genomes of hybrid plants presents an important challenge. Assemblies of heterozygous individuals, including natural tree species, require accurate handling of sequence reads to reconstruct the separate chromosome sets. For this reason, heterozygous plant genomes still pose considerable challenges in genome sequencing and assembly. An Arabidopsis F1 hybrid genome and a heterozygous grapevine accession genome were successfully de novo assembled into haplotigs using a FLACON assembler and PacBio reads [5]. Long-read sequencing technology combined with relevant assembly algorithms could help the assembly of the heterozygous genomes derived from hybridization

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