Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci.

Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (H E) and allelic richness (A R) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2-5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.

The complete plastid genome of Rhamnus taquetii, an endemic shrub on the Jeju Island of Korea.

Rhamnus taquetii (family Rhamnaceae) is a shrub , endemic to Korea. Here, the R. taquetii plastid genome was found to be 161,205 bp long and consists of quadripartite structures; a large single-copy region of 89,373 bp, a small single-copy region of 18,936 bp, and a pair of inverted repeat regions of 26,448 bp each. The GC content of the sequence was found to be 37.1%. The plastid genome was found to harbor 129 genes, including 84 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. On the phylogenetic tree of Rosales (based on 63 protein-coding genes), Rhamnaceaewas found to be monophyletic.

Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs.

Species in the genus Suaeda have few diagnostic characters and substantial morphological plasticity. Hence, regional floras do not provide clear taxonomic information for Suaeda spp. in East Asia. In order to assess the taxonomy of four species in the genus Suaeda (S. australis, S. maritima, S. japonica, and S. heteroptera), cpDNA (rpl32-trnL and trnH-psbA), nDNA (ITS), and MIG-seq analyses were carried out. Genome-wide SNP results indicated three lineages: (1) S. australis in Korea and S. maritima in Japan, (2) S. maritima in Korea and S. heteroptera in China, and (3) S. japionica. In phylogenetic trees and genotype analyses, cpDNA and nDNA results showed discrepancies, while S. japonica and S. maritima in Korea, and S. heteroptera in China shared the same haplotype and ribotype. We suggest that the shared haplotype may be due to chloroplast capture. Based on our results, we assume that S. japonica was formed by homoploid hybrid speciation between the two lineages.

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae).

Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna. Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna. However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna, whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium. Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster (trnD-GUC, trnY-GUA, and trnE-UUC). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis.

Development of 16 microsatellite markers for the Korean endemic Vicia hirticalycina (Fabaceae).

PREMISE OF THE STUDY: Vicia hirticalycina (Fabaceae) is a narrowly endemic species restricted to mountain valleys of southern Korea. To investigate its fine-scale genetic diversity and differentiation in Korea, we developed polymorphic microsatellite markers. METHODS AND RESULTS: Sixteen polymorphic microsatellite markers were developed from Illumina MiSeq data. In 74 individual plants from four populations, one to seven alleles were expressed for each locus. The levels of observed and expected heterozygosity ranged from 0.000 to 0.778 and from 0.000 to 0.738, respectively. Cross-amplification was conducted with three related species and seven to 11 markers were successfully amplified. CONCLUSIONS: These new microsatellite markers will be useful in future studies on the population genetics of V. hirticalycina.

The complete plastid genome of Suaeda malacosperma (Amaranthaceae/Chenopodiaceae), a vulnerable halophyte in coastal regions of Korea and Japan.

Suaeda malacosperma has limited distribution in the coastal regions of Korea and Japan and is named as a vulnerable halophyte in the Red List of Japan. The complete plastid genome of S. malacosperma is 151,989 bp long, and is composed of large single-copy (83,492 bp) and small single-copy (18,121 bp) regions plus two inverted repeats (25,188 bp each). The plastid genome encodes 130 genes, including 8 rRNAs, 37 tRNAs, and 83 protein-coding genes. rpl23 is pseudogenized. Phylogenetic analysis showed a sister relationship between Suaeda and Bienertia. This complete plastid genome is the first reported in genus Suaeda.

The distinct plastid genome structure of Maackia fauriei (Fabaceae: Papilionoideae) and its systematic implications for genistoids and tribe Sophoreae.

Traditionally, the tribe Sophoreae sensu lato has been considered a basal but also heterogeneous taxonomic group of the papilionoid legumes. Phylogenetic studies have placed Sophoreae sensu stricto (s.s.) as a member of the core genistoids. The recently suggested new circumscription of this tribe involved the removal of traditional members and the inclusion of Euchresteae and Thermopsideae. Nonetheless, definitions and inter- and intra-taxonomic issues of Sophoreae remain unclear. Within the field of legume systematics, the molecular characteristics of a plastid genome (plastome) have an important role in helping to define taxonomic groups. Here, we examined the plastome of Maackia fauriei, belonging to Sophoreae s.s., to elucidate the molecular characteristics of Sophoreae. Its gene contents are similar to the plastomes of other typical legumes. Putative pseudogene rps16 of Maackia and Lupinus species imply independent functional gene loss from the genistoids. Our overall examination of that loss among legumes suggests that it is common among all major clades of Papilionoideae. The M. fauriei plastome has a novel 24-kb inversion in its large single copy region, as well as previously recognized 50-kb and 36-kb inversions. The 36-kb inversion is shared by the core genistoids. The 24-kb inversion is present in the eight genera belonging to three tribes: Euchresteae, Sophoreae s.s., and Thermopsideae. The phylogenetic distribution of this 24-kb inversion strongly supports the monophyly of members of Sophoreae s.s. with Euchresteae and Thermopsideae. Hence, it can be used as a putative synapomorphic characteristic for the newly circumscribed Sophoreae, including Euchresteae and Thermopsideae. However, plastome conformation suggests a slightly narrower taxonomic group because of heterogeneous results from Bolusanthus and Dicraeopetalum. The phylogenetic analysis, based on plastome sequences from 43 legumes, represents well our understanding of legume systematics while resolving the genistoid clade as a sister group to an Old World clade. It also demonstrates the value that plastomes are powerful marker for systematic studies of basal papilionoid legumes.

Phylogeography of East Asian Lespedeza buergeri (Fabaceae) based on chloroplast and nuclear ribosomal DNA sequence variations.

The dynamic changes in land configuration during the Quaternary that were accompanied by climatic oscillations have significantly influenced the current distribution and genetic structure of warm-temperate forests in East Asia. Although recent surveys have been conducted, the historical migration of forest species via land bridges and, especially, the origins of Korean populations remains conjectural. Here, we reveal the genetic structure of Lespedeza buergeri, a warm-temperate shrub that is disjunctively distributed around the East China Sea (ECS) at China, Korea, and Japan. Two non-coding regions (rpl32-trnL, psbA-trnH) of chloroplast DNA (cpDNA) and the internal transcribed spacer of nuclear ribosomal DNA (nrITS) were analyzed for 188 individuals from 16 populations, which covered almost all of its distribution. The nrITS data demonstrated a genetic structure that followed geographic boundaries. This examination utilized AMOVA, comparisons of genetic differentiation based on haplotype frequency/genetic mutations among haplotypes, and Mantel tests. However, the cpDNA data showed contrasting genetic pattern, implying that this difference was due to a slower mutation rate in cpDNA than in nrITS. These results indicated frequent migration by this species via an ECS land bridge during the early Pleistocene that then tapered gradually toward the late Pleistocene. A genetic isolation between western and eastern Japan coincided with broad consensus that was suggested by the presence of other warm-temperate plants in that country. For Korean populations, high genetic diversity indicated the existence of refugia during the Last Glacial Maximum on the Korean Peninsula. However, their closeness with western Japanese populations at the level of haplotype clade implied that gene flow from western Japanese refugia was possible until post-glacial processing occurred through the Korea/Tsushima Strait land bridge.

Isolation and characterization of 28 microsatellite loci for a Korean endemic, Lespedeza maritima (Fabaceae).

PREMISE OF THE STUDY: We developed microsatellite primers for Lespedeza maritima (Fabaceae), a Korean endemic shrub, and conducted cross-amplifications for closely related species. METHODS AND RESULTS: We produced 28 polymorphic microsatellite markers through reference mapping of 300-bp paired-end reads obtained from Illumina MiSeq data. For 47 individual plants from two populations, the total alleles numbered two to 13, and observed and expected heterozygosities ranged from 0.067 to 0.867 and from 0.064 to 0.848, respectively. Most of these markers were well amplified in closely related species. CONCLUSIONS: In future research, the microsatellite markers described here will help reveal the taxonomic entity of this species.

Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae).

The first complete plastid genome (plastome) of the largest angiosperm genus, Astragalus, was sequenced for the Korean endangered endemic species A. mongholicus var. nakaianus. Its genome is relatively short (123,633 bp) because it lacks an Inverted Repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The putative pseudogene with abnormal stop codons is atpE. This plastome has no additional inversions when compared with highly variable plastomes from IRLC tribes Fabeae and Trifolieae. Our phylogenetic analysis confirms the non-monophyly of Galegeae.

The complete plastid genome of Piper kadsura (Piperaceae), an East Asian woody vine.

We sequenced the complete plastid genome (plastome) for Piper kadsura, a woody vine endemic to East Asia. This species is part of the largest genus within Piperaceae and its genome is almost identical to its congener P. cenocladum. The plastome for P. kadsura comprises 131 genes, including four unique rRNAs, 30 tRNAs, and 79 protein-coding genes. It retains ycf1 as an intact open reading frame. Our phylogenetic analysis demonstrated the monophyly of the Piper genus. The additional plastome sequence found in this evolutionarily and economically important genus will be a valuable, fundamental tool for future studies of phylogenetic relationships among basal angiosperms, and will provide a useful resource for molecular breeding programs.

Development of microsatellite markers for the endangered Pedicularis ishidoyana (Orobanchaceae) using next-generation sequencing.

PREMISE OF THE STUDY: Microsatellite primers were developed for Pedicularis ishidoyana (Orobanchaceae), an endangered and hemiparasitic plant that is narrowly endemic to Korea. Because its populations are threatened by loss of suitable habitat, conservation efforts are required. METHODS AND RESULTS: We developed polymorphic microsatellite loci through reference mapping of 300-bp paired-end reads obtained from Illumina MiSeq data. In all, 74 primer pairs were designed and 32 were amplified. Of these, 18 pairs were polymorphic, with two to six alleles each occurring in 26 individual plants. Expected and observed heterozygosities ranged from 0.142 to 0.703 and from 0.077 to 0.615, respectively. CONCLUSIONS: These microsatellite markers are expected to be useful for studies of the population genetics of P. ishidoyana.

Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences.

Neolitsea sericea is an evergreen broad leaved tree in the warm-temperate regions of East Asia. This area is a hotspot for plant species richness and endemism caused by dynamic changes in land configuration during the Quaternary. However, the historical migration of such evergreen tree species is still poorly understood. In an attempt to reconstruct the phylogeographic history of N. sericea during the Quaternary, we identified the chloroplast DNA haplotypes of 287 individuals from 33 populations covering almost all of its geographic range. Analyses were based on sequence data from the trnL-F, psbC-trnS, and rps16 regions. Nine haplotypes were identified. The majority included ancestral types in the southwestern part of the main islands of Japan, with other region-specific haplotypes being found in populations on the Korean Peninsula, Taiwan (Isl. Lanyu), and elsewhere in Japan. A statistical parsimony network revealed two lineages derived from Japanese main islands. One was represented on the Korean Peninsula, the other on Isl. Lanyu. The current distribution of N. sericea has been shaped by colonization via land bridges. During the glacial periods, two primary, but separate migration routes were followed--from the southwestern part of the Japanese main islands to either the Korean Peninsula or Taiwan. In addition, we believe the Zhoushan populations were shaped by post-glacial processes through an ECS land bridge (East China Sea basin) from northern refugia that existed during the late Pleistocene.

Isolation and characterization of 13 microsatellite loci from a Korean Endemic Species, Sophora koreensis (Fabaceae).

To evaluate the population genetics structure as a means of devising conservation strategies, we developed microsatellite primers for Sophora koreensis, a narrowly endemic and endangered species in Korea. Thirteen polymorphic microsatellite markers were developed in Korean populations of S. koreensis. Genetic diversity was analyzed in 40 individuals from two populations. The number of alleles per locus ranged from 4 to 14, with observed and expected heterozygosities ranging from 0.200 to 1.000 and from 0.189 to 0.864, respectively. The microsatellite markers described here are valuable tools for the population genetics research of S. koreensis. They can be used to obtain information for creating suitable management strategies to conserve this endemic and endangered species.

Isolation and characterization of 10 microsatellite loci from Korean Leontopodium japonicum (Asteraceae).

PREMISE OF THE STUDY: Microsatellite primers were developed for the alpine plant Leontopodium japonicum to evaluate its population genetics structure as a means for devising future conservation strategies. METHODS AND RESULTS: Ten polymorphic microsatellite markers were developed in Korean populations of L. japonicum. Genetic diversity was analyzed among 38 individuals from two populations. Overall, each locus had 3 to 17 alleles, and their observed and expected heterozygosities ranged from 0.0000 to 0.8750 and from 0.0000 to 0.8929, respectively. CONCLUSIONS: The microsatellite markers described here are valuable tools for population genetics research of L. japonicum. They can be used to obtain information about suitable management strategies for protecting other related and endangered "edelweiss" species.

Phylogenetic significance of stylar features in genus Vicia (Leguminosae): an analysis with molecular phylogeny.

Tribe Fabeae consists of five genera, Lathyrus (160 spp.), Lens (4-6 spp.), Pisum (2-3 spp.), Vavilovia (monotypic), and Vicia (160 spp.), and shows a diversity in stylar features. At least six different stylar types are known in the tribe. In order to reclassify the tribe at the rank of genus, we tried to discover apomorphies in stylar features using a molecular phylogenetic study. We surveyed internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA of representative species, selected from each group having different types of styles in the tribe. We paid particular attention in sampling to members of Vicia section Vicilla, as stylar features are heterogeneous within this section. Consequently, our sample set included 15 species of section Vicilla, 23 species of other Fabeae, and two species of Trifolieae, which were used as a sister group of Fabeae. Based on our analysis, we found that a laterally compressed style and an abaxially tufted hairy style would be advanced against a dorsiventrally compressed style and an evenly hairy style, respectively, in genus Vicia. The species group, which shares the latter apomorphy, is composed of 56 species and was dispersed into 11 sections of two subgenera in the recent system of genus Vicia. We consider future revision of Fabeae should treat this species group as a single higher taxon.