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Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

Citation

Cho, Myong-Suk; Kim, Seung-Chul (2021), Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation , Dryad, Dataset, https://doi.org/10.5061/dryad.x3ffbg7jn

Abstract

Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, Prunus takesimensis Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, P. sargentii distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor. However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of P. takesimensis using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of P. takesimensis, (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor), (3) the geographic origin of P. takesimensis via single introduction from source population of P. sargentii in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species P. takesimsnsis compared to continental progenitor P. sargentii, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.

Usage Notes

1. Data 1_123 Prunus_ITS_ETS.nex

Alignment of two concatenated nuclear DNA ITS and ETS regions in nexus format for ITS/ETS phylogeny (123 accessions and aligned 956 characters).

2. Data 2_123 Prunus_7CP.nex

Alignment of seven concatenated chloroplast DNA regions in nexus format (petA-psbJ, petD-rpoA, ndhF-rpl32, trnQ-rps16, trnV-ndhC, rpl16 intron, and trnL-rpl32 regions) for cpDNA phylogeny (123 accessions and 5,414 characters).

3. Data 3_99 SA_TA_5cp.phy

Alignment of five concatenated chloroplast DNA regions (petA-psbJ, petD-rpoA, trnQ-rps16, rpl16 intron, and trnL-rpl32 regions) including 13 populations of P. takesimensis from Ulleung Island (69 accessions) and 5 populations of P. sargentii (30 accessions) collected from its adjacent areas in phylip format for TCS cpDNA haplotype network (99 accessions and 3,809 characters).

4. Data 4_262 Prunus_SNP.phylip.txt

SNPs generated by Stacks v1.48 from multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) dataset in phylip format for genome-wide SNP phylogeny (262 accessions and 5899 SNPs).

5. Data 5_262 Prunus.vcf

Details of variant sites of multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) dataset generated by Stacks v1.48 in variant call format (vcf) for principal component analysis (PCA) analysis for 262 accessions.

6. Data 6_262 Prunus_structure.txt

SNPs of multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) dataset generated by Stacks v1.48 in the STRUCTURE input file format for genetic structure analysis (262 accessions and SNPs from 8527 loci).

 

7. Data 7_200 TA_SA_structure.txt

SNPs of multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) dataset including 14 populations of P. takesimensis and five populations of P. sargentii generated by Stacks v1.48 in the STRUCTURE input file format for genetic structure analysis (200 accessions and SNPs from 7038 loci).

Funding

National Research Foundation of Korea, Award: 2019R1A6A1A10073079