Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses.

BACKGROUND: The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea. RESULTS: The average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports. CONCLUSIONS: Our study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.

Genetic diversity patterns and domestication origin of soybean.

KEY MESSAGE: Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary history of soybean. Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States.

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes.

Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.

Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed (Hypochaeris radicata).

Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model-based approaches to characterize the invasion dynamics of Hypochaeris radicata L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent-based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model-based approaches. Our data suggest that H. radicata has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human-mediated dispersal. Our study represents the first population-level genomic research documenting the invasion dynamics of the successful worldwide invader, H. radicata, outside of Europe.

Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species.

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.

Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea.

Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.

The complete chloroplast genome of Euphorbia prostrata (Euphorbiaceae).

Euphorbia prostrata Aiton 1789, an annual herb, is native to tropical and subtropical Americas and was introduced into many parts of the Old-World including Korea. We determined the genomic characteristics of the complete chloroplast genome of E. prostrata with a de novo assembly strategy. The complete chloroplast genome was 162,858 bp long, and harbored 86 protein coding, 37 tRNA and 8 rRNA. The genome showed the typical quadripartite structure consisting of a large single copy (LSC) (90,580 bp), a small single copy (SSC) (18,570 bp) and a pair of inverted repeats (IRs) (26,854 bp). The phylogenetic tree inferred from chloroplast genomes of 25 taxa, which belong to Euphorbiaceae indicated that the Euphorbia is a monophyletic group and E. prostrata is closely related with E. humifusa, E. thymifolia and E. hirta, forming a well-supported clade. Our findings can be valuable for understanding the phylogenetic relationships and the evolution in Euphorbiaceae and will provide basic information for future studies on E. prostrata from genomic perspective.

Adaptive divergence for a drought resistance related trait among invasive Saltcedar (Tamarix L.) populations in southwestern US: Inferences from QCT - FCT.

Biological invasion poses several biotic and abiotic challenges due to abrupt distribution shifts. Invasive species may benefit from local adaptation responding to environmental stresses during colonization. Saltcedar (Tamarix), a notorious invasive shrub in the western US introduced from Eurasia may have adapted to low rainfall as the species widely occupies the arid land throughout the southwestern US. We investigated variation of quantitative traits in saltcedar between two regions exhibiting opposing average annual precipitations under experimentally manipulated water treatments to test local adaptation. We measured eight quantitative traits, proxies for fitness and genotyped 64 individual samples using genotype by sequencing technique. To test local adaptation, we applied QCT - FCT test based on null distribution of FCT estimated from 2,697 genome-wide SNPs and QCT estimated for the eight phenotypic traits measured. Saltcedar in the southwestern US exhibited a significant interaction between the degree of leaf loss (biomass loss by senesced leaves to total biomass) under simulated drought conditions and the origins from which the genotypes were collected, either relatively high or low rainfall regimes. The divergence found in leaf loss was significantly greater among regions than the expected given the genetic divergence on neutral loci suggesting signature of local adaptation responding to drought. The results demonstrate adaptive potential of saltcedar populations to extreme drought. As extreme aridity is often predicted in climate models across the southwestern US, the western saltcedar genotypes locally adapted to drought may further expand their ranges in this region.

Genetic diversity pattern reveals the primary determinant of burcucumber (Sicyos angulatus L.) invasion in Korea.

Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.

Genetic Diversity on a Rare Terrestrial Orchid, Habenaria linearifolia in South Korea: Implications for Conservation Offered by Genome-Wide Single Nucleotide Polymorphisms.

Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high F ST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.

Phedimusdaeamensis (Crassulaceae), a new species from Mt. Daeam in Korea.

Phedimus individuals from Mt. Daeam, once referred to as Phedimussikokianus, exhibit certain morphological characters that are unique within the genus. Phedimus is one of the most notorious groups for taxonomic problems due to the high morphological variation found in leaf shape, stem numbers, phyllotaxis and seed structure. Taxa in Phedimus also easily hybridize, further leading to taxonomic confusion. To carefully confirm the identity of the putative new species from Mt. Daeam, we examined morphological characters from ~100 herbarium sheets of six closely related Phedimus species. A molecular phylogenetic approach was also employed to delimit the species boundary and infer the phylogenetic relationships among the seven Phedimus species, including the species from Mt. Daeam. Both morphological and molecular phylogenetic results indicated that the species found on Mt. Daeam is a new species that is more closely related to P.middendorffianus and P.takesimensis than to the remaining four Phedimus species. Here, we provided a full description of the new species P.daeamensis as well as an updated key for the seven Phedimus species examined.

The complete chloroplast genome sequences of the Sicyos angulatus (Cucurbitaceae).

Sicyos angulatus (burcucumber) is an annual plant native to the north-eastern America. We investigated the genomic characteristics of the complete chloroplast (CP) genome in S. angulatus with a de novo strategy. The CP genome was 154,986 bp in length including 84 protein coding genes, 37 tRNA genes, and eight rRNA genes. It has large single-copy (LSC) (84,355 bp), small single-copy (SSC) (18,079 bp), and a pair of inverted repeats (IRs) (26,276 bp), which consists of typical quadripartite structure. A phylogenetic analysis of 64 CP genomes from Cucurbitaceae revealed that the Sicyos angulatus was separated from other species and clustered together with Sicyos edulis, which is congruent with previous studies. Infrafamilial classification system inferred from our data was also congruent with previous study based on CP DNA data.

Genetic Admixture in the Population of Wild Apple (Malus Sieversii) from the Tien Shan Mountains, Kazakhstan.

There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.

The complete chloroplast genome sequences of the Rosa kokanica (Regel) Regel ex Juz. (Rosaceae).

Rosa kokanica is a deciduous shrub distributed in Central Asia. We determined the genomic characteristics of the complete chloroplast genome in R. kokanica with a de novo assembly strategy. The chloroplast genome was 156,802bp in length harboring 89 protein coding genes, 37 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (85,899bp), a small single-copy (SSC) (18,773bp) and a pair of inverted repeats (IRs) (26,065bp). Phylogenetic analysis of 16 chloroplast genomes from Rosaceae revealed that the genus Rosa is a monophyletic group and the R. kokanica is clustered together with the congener, R. acicular.

The complete chloroplast genome sequences of the Iris loczyi kanitz (Iridaceae).

Iris loczyi is a perennial rhizomatous herb distributed in Central Asia. We examined genomic architecture of the complete chloroplast genome in I. loczyi by assembling the Illumina MiSeq reads using de novo strategy. The chloroplast genome is 150,940 bp in length harboring 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. It exhibits typical quadripartite structure comprising LSC (80,907 bp), SSC (17,853 bp), and a pair of IRs (26,090 bp). Phylogenetic analysis of 20 chloroplast genomes from Asparagales revealed that Iridaceae is a monophyletic group and the I. loczyi is clustered together with the congener, I. sanguinea.

An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea.

Range-wide population studies of wide spread species are often associated with complex diversity patterns resulting from genetically divergent evolutionary significant units (ESUs). The compound evolutionary history creating such a pattern of diversity can be inferred through molecular analyses. Asparagus cochinchinensis, a medicinally important perennial herb, is in decline due to overharvesting in Korea. Eight A. cochinchinensis populations in Korea and three populations from neighboring countries (China, Japan and Taiwan) were examined using nine nuclear microsatellite loci and three chloroplast microsatellite loci to characterize molecular diversity patterns. The average within-population diversity was limited likely due to long-term bottlenecks observed in all eight populations. High pairwise FST values indicated that the populations have largely diverged, but the divergences were not correlated with geographic distances. Clustering analyses revealed a highly complex spatial structure pattern associated with two ESUs. Approximate Bayesian Computation (ABC) suggests that the two ESUs split about 21,000 BP were independently introduced to Korea approximately 1,800 years ago, and admixed in secondary contact zones. The two ESUs found in our study may have different habitat preferences and growth conditions, implying that the two genetically divergent groups should be considered not only for conservation and management but also for breeding programs in agricultural areas.

Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations.

Distribution of genetic variation over time and space is relevant to demographic histories and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used eight microsatellite markers to examine the level of genetic diversity, spatial structure, and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within-population genetic variation associated with historical bottlenecks. Although pairwise F ST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broadscale spatial pattern of genetic structure. Bayesian clustering (best K = 6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045) and historical migration rates (2 × e-5-4.6 × e-4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.

Development and characterization of 30 microsatellite loci for Plagiorhegma dubium (Berberidaceae).

PREMISE OF THE STUDY: Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats. In this study, 30 microsatellite loci, including 25 polymorphic loci, were developed for P. dubium for use in population-level genetic analyses. METHODS AND RESULTS: We carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag-simple sequence repeat markers from P. dubium using Illumina HiSeq high-throughput sequencing. To test utility of the developed markers, we genotyped 60 individuals from three populations and estimated the number of alleles and levels of observed and expected heterozygosity. Expected heterozygosity levels ranged from 0.000 to 0.594, 0.000 to 1.000, and 0.000 to 0.744 in the three populations, respectively. CONCLUSIONS: These transcriptome-derived simple sequence repeat markers are highly polymorphic and can be widely used in characterization of the endangered P. dubium. Population genetic studies with these markers will provide valuable insights for conservation by unraveling evolutionary patterns of P. dubium.

Genetic diversity and structure of an endangered medicinal herb: implications for conservation.

Human-driven habitat fragmentation leads to spatial isolation of endangered plant species increasing extinction risk. Understanding genetic variability and population structure of rare and isolated plant species is of great importance for assessing extinction risk and setting up conservation plans. Aconitum austrokoreense, an endangered and endemic species in Korea, is a perennial herb commonly used for medicinal purposes. We used five nuclear microsatellites and one chloroplast marker to investigate genetic diversity and population structure for 479 individuals of A. austrokoreense from seven populations throughout South Korea. A multivariate approach, discriminant analysis of principal components analysis, revealed broad-scale spatial patterns of A. austrokoreense populations across three major mountains that were composed of seven genetically distinct subgroups. High pairwise FST values (mean FST = 0.35; highest FST = 0.55) suggested significant differentiation among populations. Overall within population genetic variation was low. Based on Mantel test, there was significant correlation between geographical and genetic distances indicating pattern of isolation by distance. Our results suggest that A. austrokoreense populations may have undergone recent population bottlenecks. Given the limited dispersal ability of the species and ongoing habitat fragmentation, population isolation may further be exacerbated leading to increased extinction risk.