DOI: 10.5061/dryad.cz8w9gj02
title: Multiple lines of evidence for independent origin of wild and cultivated flowering cherry (Prunus yedoensis)

description: As with many other ornamental and cultivated plants that have been under
 human selection and cultivation for a long time, it has been a major
 challenge to trace back the complex evolutionary history of flowering
 cherry, Prunus yedoensis. This challenge has been further amplified by
 great morphological similarities, little molecular divergence, frequent
 natural and artificial hybridization, and poor documentation of breeding
 history among cultivated and wild flowering cherries. The origin and
 taxonomic distinction between wild P. yedoensis from Jeju Island, Korea,
 and one of the most popular cultivated flowering cherries, P. × yedoensis
 ‘Somei-yoshino’ has been a controversy for the past few decades. We
 sampled many areas extensively, and using four different molecular markers
 we provided evidence for their independent origin. Wild P. yedoensis in
 Korea originated from multiple bidirectional hybridization events between
 two sympatric species, P. spachiana f. ascendens as the maternal species
 and P. serrulata var. spontanea/P. serrulata var. quelpaertensis as the
 most probable paternal species. On the contrary, our results supported a
 single artificial hybrid origin of P. × yedoensis ‘Somei-yoshino’ from
 cultivated P. spachiana f. ascendens as the maternal species and P.
 speciosa, a species endemic to Izu Islands, as the paternal species. Based
 on extensive sampling, we provided strong evidence that wild and
 cultivated P. yedoensis are distinct taxonomic entities that have
 originated from different evolutionary processes. A potential for the
 development of new cultivars from wild P. yedoensis and conservation of
 diverse germplasms in situ insular setting and ex situ should be explored
 in the future.
description: Alignment of seven concatenated chloroplast DNA regions in nexus
 format (<i>pet</i>A-<i>psb</i>J,
 <i>pet</i>D-<i>rpo</i>A,
 <i>ndh</i>F-<i>rpl</i>32,
 <i>trn</i>Q-<i>rps</i>16,
 <i>trn</i>V-<i>ndh</i>C, <i>rpl</i>16
 intron, and <i>trn</i>L-<i>rpl</i>32 regions) for
 cpDNA phylogeny (194 accessions and 5,547 characters).
 Data1_7cp concatenated.nex Alignment of nuclear DNA ITS region in nexus format for ITS phylogeny (a total of 322 accessions of 178 direct and 144 cloned sequences and 600 characters). Data2_ITS.nex Alignment of four concatenated nuclear RosCOS loci (RosCOS 00517, 03628, 01167, and 01445) in nexus format for single nucleotide polymorphisms (SNPs) analysis and split graph networking (a total of 87 accessions and 1,250 characters). Data3_RosCOS 4 loci.nex Alignment of <i>PolA1 </i>PI19 intron data sets in nexus format for single nucleotide polymorphisms (SNPs) analysis (a total of 72 accessions; 25 accessions of cloned sequences and directly sequenced 41 accessions and 630 characters). Data4_POLA1 PI19-1 intron.nex Alignment of <i>PolA1 </i>PI21 intron data sets in nexus format for single nucleotide polymorphisms (SNPs) analysis (a total of 47 accessions and 764 characters). Data5_POLA PI21 intron.nex Alignment of five concatenated chloroplast DNA regions in nexus format (<i>pet</i>B-<i>pet</i>D, <i>pet</i>D-<i>rpo</i>A, <i>trn</i>S-<i>trn</i>G, <i>rpl</i>16, and <i>ycf</i>1) for chloroplast haplotype network analysis (a total of 105 accessions and 2,826 characters). Data6_5cp concatenated.nex