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.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1497-y) contains supplementary material, which is available to authorized users.

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[1] Kuroshio velocity structure and transport in the East China Sea (ECS) were investigated as part of a 23-month study using inverted echo sounders and acoustic Doppler current profilers (ADCPs) along the regularly sampled PN-line. Flow toward the northeast is concentrated near the continental shelf with the mean surface velocity maximum located 30 km offshore from the shelf break (taken as the 170 m isobath). There are two regions of southwestward flow: a deep countercurrent over the continental slope beneath the Kuroshio axis and a recirculation offshore which extends throughout the whole water column. There is a bimodal distribution to the depth of maximum velocity with occurrence peaks at the surface and 210 dbar. When the maximum velocity is located within the top 80 m of the water column, it ranges between 0.36 m/s and 2.02 m/s; when the maximum velocity is deeper than 80 m, it ranges between 0.31 m/s and 1.11 m/s. The 13-month mean net absolute transport of the Kuroshio in the ECS is 18.5 ± 0.8 Sv (standard deviation, s = 4.0 Sv). The mean positive and negative portions of this net flow are 24.0 ± 0.9 Sv and À5.4 ± 0.3 Sv, respectively.

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Pacific Decadal Oscillation (PDO) index is strongly correlated with vertically integrated transport carried by the Kuroshio through the East China Sea (ECS). Transport was determined from satellite altimetry calibrated with in situ data and its correlation with PDO index (0.76) is highest at zero lag. Total PDO‐correlated transport variation carried by the ECS‐Kuroshio and Ryukyu Current is about 4 Sv. In addition, PDO index is strongly negatively correlated, at zero lag, with NCEP wind‐stress‐curl over the central North Pacific at ECS latitudes. Sverdrup transport, calculated from wind‐stress‐curl anomalies, is consistent with the observed transport variations. Finally, PDO index and ECS‐Kuroshio transport are each negatively correlated with Kuroshio Position Index in the Tokara Strait; this can be explained by a model in which Kuroshio path is steered by topography when transport is low and is inertially controlled when transport is high.