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

First author: Seunghoon Baek; Affiliations: Myongji University (明知大学): Yongin, Korea

Corresponding author: Jeong-Hwan Mun

Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus (李属) includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics (观赏特性) 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. 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. yedoensisis an F1 hybrid originating from a cross between maternal P. pendula f. ascendens (江户彼岸) and paternal P. jamasakura (日本山樱), and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes (单倍型) of closely related taxa distributed in a sympatric (同域的) natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility (配子体自交不亲和性) is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm (混合群). 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.

杂交是演化过程中增加植物物种多样性的一个重要来源。李属植物包含众多樱桃类物种，因其花色而闻名世界。这些植物的观赏特性通过自然和人工杂交所获得。因此，杂交李属植物不仅在植物基因组上，还在生物演化上存在难以克服的困难。作者利用三代测序技术对高度杂合的李属植物染井吉野樱进行了全基因组测序和组装。基因组组装共覆盖了93％的基因区，注释到了41294个蛋白编码基因。与近缘的16个物种的比较基因组分析显示约有41%的基因能够知道其来自于母本或者父本。这说明染井吉野樱由母本江户彼岸和父本日本山樱的杂交而成，其余日本樱花能够很好的区分开来。对于天然分布上存在重叠的近缘物种的S单倍型分析显示物种间杂交的限制减小导致了强烈的配子体自交不亲和性，可能促进了野生李属植物杂交的复杂性及混合群的形成。本文通过三代测序技术和基因组分型技术报道了天然杂交李属植物的基因组草图。基于其与近缘物种的综合比较基因组学分析，研究显示分布上存在重叠的物种种间杂交促进了开花植物李属物种的分化。

p.s. S位点基因通常以一个单位遗传给后代，几乎不会发生重组现象，因此又叫做S单倍型。

doi: https://doi.org/10.1186/s13059-018-1497-y

Journal: Genome Biology

Published date: 04 September, 2018

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