DOI: 10.5061/dryad.dncjsxkzk
title: Data from: Phylogenetic origin of two Japanese Torreya taxa found in two regions with strongly contrasting snow depth

description: The Japanese archipelago exhibits a notable difference in snow depth in
 winter, deep snow on the Sea of Japan side and low snow cover on the
 Pacific Ocean side. This contrasting pattern has shaped the distribution
 of infraspecific taxon pairs in a range of woody plants, with taxa found
 on the Sea of Japan side typically exhibiting a stunted shrub form with
 multiple decumbent stems. The phylogenetic origin of these taxon pairs is
 unknown, i.e., whether the two taxa diverged from the same species or if
 they have different origins. This study aimed to reveal the phylogenetic
 origin of two varieties of Torreya nucifera (Taxaceae); var. nucifera is a
 tree found on the Pacific Ocean side, whereas var. radicans is a shrub
 found on the Sea of Japan side. We examined the phylogenetic relationships
 of the two varieties and worldwide Torreya taxa using whole chloroplast
 genomes, chloroplast DNA fragments, and the nuclear ribosomal internal
 transcribed spacer (ITS). The whole chloroplast genome phylogeny indicated
 that T. nucifera var. radicans was a sister taxon to Chinese T. grandis,
 rather than to var. nucifera. In contrast, the nuclear ITS phylogeny
 indicated that while several haplotypes of T. nucifera var. radicans were
 closely related to T. grandis, most haplotypes of T. nucifera var.
 radicans formed a single clade with those of var. nucifera. This implies
 that the homogenization of the ITS has occurred between the two taxa,
 while taxon-specific chloroplast DNA haplotypes were retained. These
 discordant phylogenies suggested that the two taxa have different
 phylogenetic origins, but have an intricate evolutionary history,
 involving inter-taxa hybridization and gene flow, possibly when their
 distributions were confined to sympatric refugia. Given the genetic
 evidence and distinct difference in growth form, we propose that T.
 nucifera var. radicans should be taxonomically treated as a distinct
 species, T. fruticosa.
description: We assembled draft whole
 chloroplast genomes for phylogenetic analysis of one T. nucifera var.
 nucifera from Shiiba, Miyazaki Prefecture, Kyushu, Japan (SB3) and two T.
 nucifera var. radicans from Naramata, Gunma Prefecutre (NM2) and Otari,
 Nagano Prefecture (OTA4), Honshu, Japan. A total of between 1.5–2.9 μg of
 DNA was sent to the Beijing Genomics Institute where short-size DNB-seq
 libraries were constructed and paired-end sequencing (2×150 bp) was
 performed on an Illumina HiSeq2000 Genome Analyzer resulting in
 approximately 1 G of data per sample. We constructed the whole chloroplast
 genome for the three samples using a mapping read to reference approach
 (Bernhardt et al. 2017) in CLC Genomics Workbench using the South Korean
 T. nucifera var. nucifera whole chloroplast genome (MK978775) (Shin et al.
 2019) as a reference. Read mapping was undertaken using default settings
 and a consensus sequence extracted using a minimum read depth threshold of
 10 whereby positions under 10 were scored as ambiguous Ns, conflict
 resolution strategy set to vote and use quality score set to
 yes.
description: Data:
 Torreya_nucifera_var._nucifera_SB3_draft_whole_chloroplast_genome.fa<br> Torreya_nucifera_var._radicans_NM2_draft_whole_chloroplast_genome.fa<br> Torreya_nucifera_var._radicans_OTA4_draft_whole_chloroplast_genome.fa Details are shown in Table 4 in our original paper.