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Abstract Background Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species. Results This study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary. Conclusions The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species.

Ajuga spectabilis Nakai is a Korean endemic species in Lamiaceae. In spite of its importance, genomic studies are not performed on this species. Here, we report the complete plastid genome sequences of A. spectabilis, which will provide valuable information for its natural conservation and future studies for the plastid genome evolution. The plastid genome is 150,417 bp in length, containing a large single-copy region (LSC) of 82,140 bp and a small single-copy (SSC) region of 17,165 bp which are separated by a pair of inverted repeats (IR) of 25,556 bp. It encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content is 38.3%, and those in the LSC, SSC, and IR regions are 36.4%, 32.2%, and 43.3%, respectively, which is consistent with other Ajuga species. Our phylogenetic analysis revealed that A. spectabilis formed a close relationship with A. ciliata and A. decumbens.

Plastome sequences are crucial in plant studies due to their role in examining genomic evolution, understanding phylogenetic relationships, and developing molecular markers. Despite the collection of information about Korean figs, their genomic data remain underexplored. We utilize next-generation sequencing and PCR techniques to investigate genomic data and to develop and validate molecular markers. In this study, we characterize the complete plastomes of Korean figs: F. erecta, F. erecta var. sieboldii, F. sarmentosa var. nipponica, and F. sarmentosa var. thunbergii, which range in length from 160,276 to 160,603 bp. These genomes comprise 78 plastid protein-coding genes, 30 tRNA, and four rRNA, with the exception of one pseudogene, infA. We discovered that F. erecta and F. erecta var. sieboldii share identical plastome sequences. Phylogenomic analysis indicates the monophyly of Ficus, although the relationships among its subgenera remain unclear. We discovered that Ficus possesses 467 molecular diagnostic characters in its plastid protein-coding genes compared to other Moraceae groups, and F. erecta exhibits 33 molecular diagnostic characters. Single nucleotide polymorphisms in ndhD, petA, and rbcL were effectively used to develop molecular markers for distinguishing F. erecta from other figs. Additionally, we provided a straightforward PCR protocol for utilizing these newly developed molecular markers.

Abstract This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies—Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae—which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies—Crocoideae, Nivenioideae, and Aristeoideae—shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

Understanding of intercontinental distribution in the Northern Hemisphere has attracted a lot of attention from botanists. However, although Orchidaceae is the largest group of angiosperms, biogeographical studies on the disjunctive pattern have not been sufficient for this family. Goodyera R. Br. (tribe Cranichideae, subfamily Orchidoideae, family Orchidaceae) is widely distributed in temperate and tropical regions. Although the phylogenetic relationship of Goodyera inferred from both morphological and molecular data has been conducted, the sampled taxa were mainly distributed in Asia regions that resulted in non-monophyly of this genus. In this study, the complete plastid genomes of Goodyera, generated by next-generation sequencing (NGS) technique and sampled in East Asia and North America, were used to reconstruct phylogeny and explore the historical biogeography. A total of 18 Goodyera species including seven newly sequenced species were analyzed. Based on 79 protein-coding genes, the phylogenetic analysis revealed that Goodyera could be subdivided into four subclades with high support values. The polyphyletic relationships among Goodyera taxa were confirmed, and the unclear position of G. foliosa was also resolved. The datasets that are composed of the 14 coding sequences (CDS) (matK, atpF, ndhK, accD, cemA, clpP, rpoA, rpl22, ndhF, ccsA, ndhD, ndhI, ndhA, and ycf 1) showed the same topology derived from 79 protein-coding genes. Molecular dating analyses revealed the origin of Goodyera in the mid-Miocene (15.75 Mya). Nearctic clade of Goodyera was diverged at 10.88 Mya from their most recent common ancestor (MRCA). The biogeographical reconstruction suggests that subtropical or tropical Asia is the origin of Goodyera and it has subsequently spread to temperate Asia during the Miocene. In addition, Nearctic clade is derived from East Asian species through Bering Land Bridge (BLB) during the Miocene. The speciation of Goodyera is most likely to have occurred during Miocene, and climatic and geological changes are thought to have had a part in this diversification. Our findings propose both origin and vicariance events of Goodyera for the first time and add an example for the biogeographical history of the Northern Hemisphere.

Abstract Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.

Abstract The high genetic diversity of rear‐edge refugia populations is predicted to have resulted from species repeatedly migrating to low latitudes during glacial periods over the course of Quaternary climate change. However, several recent empirical studies of cold‐tolerant plants revealed the opposite pattern. We investigated whether current habitats of the cold‐adapted and range‐restricted Bupleurum euphorbioides in the Baekdudaegan, South Korea, and North Korea could be interglacial refugia, and documented how their rear‐edge populations differ genetically from those of typical temperate species. Phylogeographic analysis and ecological niche modeling (ENM) were used. The genetic structure was analyzed using microsatellite markers and chloroplast DNA sequences. The congener B. longiradiatum was included as a typical temperate plant species. Despite having almost identical life history traits, these congeneric species exhibited contrasting patterns of genetic diversity. ENM revealed an apparent maximum range contraction during the last interglacial. In contrast, its range expanded northward to the Russian Far East (Primorsky) during the Last Glacial Maximum. Thus, we hypothesize that B. euphorbioides retreated to its current refugia during interglacial periods. Unlike populations in the central region, the rear‐edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. The rear‐edge B. euphorbioides survived at least one past interglacial, contributing to the species’ genetic diversity. We believe that such genetic variation in the cold‐adapted B. euphorbioides gives the species the necessary adaptations to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change.

Abstract Discoid lateral meniscus (DLM) is a common anatomic variant in the knee typically presented in young populations, with a greater incidence in the Asian population than in other populations. As DLM is a congenital anomaly, the ultrastructural features and morphology differ from those of the normal meniscus, potentially leading to meniscal tears. Snapping and pain are common symptoms, with occasional limitations of extension, in patients with DLM. Examination of the contralateral knee is necessary as DLM affects both knees. While simple radiographs may provide indirect signs of a DLM, magnetic resonance imaging (MRI) is essential for diagnosis and treatment planning. Although DLM was traditionally classified into three categories, namely, complete, incomplete, and Wrisberg DLM, a recent MRI classification provides useful information for surgical planning because the MRI classification was based on the peripheral detachment in patients with DLM, as follows: no shift, anterocentral shift, posterocentral shift, and central shift. Asymptomatic patients require close follow-up without surgical treatment, while patients with symptoms often require surgery. Total or subtotal meniscectomy, which has been traditionally performed, leads to an increased risk of degenerative arthritis; thus, partial meniscectomy is currently considered the treatment of choice for DLM. In addition to partial meniscectomy, meniscal repair of peripheral detachment is recommended for stabilization in patients with DLM to preserve the function of the meniscus. Previous studies have reported that partial meniscectomy with or without meniscal repair is effective and shows superior clinical and radiological outcomes to those of total or subtotal meniscectomy during the short- to long-term follow-up. Our preferred principle for DLM treatment is reduction, followed by reshaping with reference to the midbody of the medial meniscus and repair as firm as possible.

Scientists have long been captivated by biogeographic disjunctions, and disjunctions between East Asia and North America have been particularly well-studied at the genus and family levels. By contrast, disjunctions between eastern and western Asia have received less attention. Euonymus L. is taxonomically divided into two sections based on the number of cells in anthers as follows: E. sect. Uniloculares has one-celled anthers and occurs mainly in Asia, whereas E. sect. Biloculares has two-celled anthers and is distributed globally. We used Illumina sequencing to investigate the genomes of four species in sect. Uniloculares. The chloroplast (cp) genomes are highly conserved (157,290–158,094 bp). Pseudogenisation of ndhF and intron loss in rps16 was detected. Based on the cp genomes of the four species of E. sect. Uniloculares, we propose a novel hypothesis of disjunction between eastern and western Asia. Biogeographic reconstruction and molecular dating revealed that sect. Uniloculares separated from its sect. Biloculares forebears 4.0 Mya during the Pliocene era. The radial diversification of sect. Uniloculares from East Asia and the establishment of the western Asian clade during the Pleistocene era (1.9 Mya) were the results of both dispersal and vicariance, making the section the youngest diverged clade conforming to age estimation. The centre of origin of sect. Uniloculares was determined to be in East Asia. Disjunctions and diversification between eastern and western Asia in sect. Uniloculares are thought to have been caused by changes in monsoon patterns, temperature variations, and the emergence of the Gobi Desert.

Background: Hip resurfacing arthroplasty (HRA) may be a suitable option for treating osteonecrosis of the femoral head (ONFH). However, concerns regarding the extent of osteonecrosis, amount of defect under the prosthesis, and implant-related complications remain. This study aimed to report implant-specific outcomes and risk factors for failure of HRA in ONFH. Methods: A total of 202 HRAs (166 patients) performed by a single surgeon were investigated. The stage, size, and location of ONFH were evaluated using preoperative radiographs and magnetic resonance images. Clinical, radiographic results, and serum metal concentrations of articular surface replacement (ASR) and non-ASR devices were compared. Logistic regression analysis was performed to identify the contributors of failures. The mean follow-up duration was 10.6 years. Results: Twenty-six hips (12.9%) were operated with Birmingham Hip Resurfacing (BHR), 99 (49.0%) with ASR, and 77 (38.1%) with Conserve Plus. The mean Harris Hip Score improved from 52.1 to 93.2 at the final follow-up (P

Osteoarthritis (OA) is a chronic degenerative joint disease accompanied by an inflammatory milieu that results in painful joints. The pathogenesis of OA is multifactorial, with genetic predisposition, environmental factors, and traumatic injury resulting in the direct or indirect loss of cartilage. The articular cartilage can also be damaged by direct focal traumatic injury. Articular cartilage provides a smooth, deformable bearing surface with a low coefficient of friction, increased contact area, and reduced contact stress. Articular type II hyaline cartilage lines the synovial joints and, when injured, has a limited ability for repair, except for the most superficial layers via diffusion from the synovial fluid, secondary to no blood supply, a complex structure, and a low metabolic rate. Restoring the articular surface can relieve pain and restore function. Although many strategies have been developed to regenerate type II collagen based on the extent of the lesion, surgical treatments are still evolving. The peroxisome proliferator-activated receptor delta (PPARδ) agonist and collagen treatment of mesenchymal stem cells (MSCs) enhance the chondrogenic capacity in vitro. We present a novel technique for cartilage restoration in a rabbit cartilage osteochondral defect model using a PPARδ agonist (GW0742)-infused 3D collagen scaffold to induce type II cartilage from MSCs.

Alzheimer’s disease (AD) pathogenesis is linked to amyloid plaque accumulation, neuronal loss, and brain inflammation. Ficus erecta Thunb. is a food and medicinal plant used to treat inflammatory diseases. Here, we investigated the neuroprotective effects of F. erecta Thunb. against cognitive deficit and neuronal damage in a mouse model of amyloid-β (Aβ)-induced AD. First, we confirmed the inhibitory effects of ethanol extracts of F. erecta (EEFE) leaves on Aβ aggregation in vivo and in vitro. Next, behavioral tests (passive avoidance task and Morris water maze test) revealed EEFE markedly improved cognitive impairment in Aβ-injected mice. Furthermore, EEFE reduced neuronal loss and the expression of neuronal nuclei (NeuN), a neuronal marker, in brain tissues of Aβ-injected mice. EEFE significantly reversed Aβ-induced suppression of cAMP response element-binding protein (CREB) phosphorylation and brain-derived neurotrophic factor (BDNF) expression, indicating neuroprotection was mediated by the CREB/BDNF signaling. Moreover, EEFE significantly suppressed the inflammatory cytokines interleukin 1beta (IL-1β) and tumor necrosis factor alpha (TNF-α), and expression of ionized calcium-binding adaptor molecule 1 (Iba-1), a marker of microglial activation, in brain tissues of Aβ-injected mice, suggesting anti-neuroinflammatory effects. Taken together, EEFE protects against cognitive deficit and neuronal damage in AD-like mice via activation of the CREB/BDNF signaling and upregulation of the inflammatory cytokines.

Medial meniscus posterior root tear is a disruptive injury causing significant sequelae. Several techniques to repair and maintain the native function of the medial meniscus have been introduced, but limitations have been reported in terms of their results. In this current note, the authors introduce the arthroscopic transtibial pull-out repair with whip running suture technique, which may not only avoid the potential risk of meniscus cut-through by the suture material but also optimize the reduction of the extruded meniscus. By suturing the posteromedial capsule and peripheral meniscus, more medialization force can be directly applied to the extruded part of the meniscus, and normal hoop tension can be restored.

Habenaria cruciformis (Orchidaceae), endemic to South Korea, is a perennial herb and its local population sizes are declined because of the destruction caused by human activity and the invasion of exotic species in their habitats. Here, we report the complete chloroplast (cp) genome sequence of H. cruciformis, which will provide valuable information for its biological conservation and future studies for the cp genome evolution of endemic plants on the Korean Peninsula. The cp genome of H. cruciformis is 155,708 bp in length, containing a large single-copy region of 85,131 bp and a small single-copy region of 17,659 bp which are separated by a pair of inverted repeats of 26,459 bp. The H. cruciformis cp genome encodes 131 genes, of which 113 are unique, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 36.6%, which is consistent with the Habenaria species previously reported. Our phylogenomic analyses identified the sister relationship between H. cruciformis and H. linearfolia in the genus.

Prunus × nudiflora is an endemic species to Jeju Island, South Korea and economically important as ornamentals. According to recent molecular phylogenetic and genomic studies, this species is revealed as a F1 hybrid originating from a cross between maternal Prunus pendula f. ascendens and paternal Prunus jamasakura. However, the plate specimen designated as type materials of P. × nudiflora does not permit a precise application of the name because of its poor condition. The herbarium specimens related with that illustration were examined to clarify the identity of P. × nudiflora, and an epitype is selected. Our epitypification proposed here will ensure nomenclatural accuracy for most material from cultivation, where the name P. × nudiflora is widely used. Keywords: Epitypification, Endemic species, Prunus × nudiflora, Rosaceae, South Korea

Abstract Background This meta-analysis was designed to quantify adduction moment loss, to evaluate the relationship between changes in mechanical axis alignment and adduction moment, and to assess whether sagittal plane moment is altered after medial open wedge high tibial osteotomy (HTO). Methods Following preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, all studies reporting preoperative and postoperative peak knee adduction moment or change in peak knee adduction moment from before to after surgery in patients who underwent medial open wedge HTO were included. Results Nine studies were included in the meta-analysis. The pooled mean difference in adduction moment from before to after medial open wedge HTO was 1.44% Nm/body weight (BW)xheight (HT) (95% confidence interval [CI]: 1.33 to 1.55% Nm/BWxHT; P

Abstract Background Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. Results We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm. Conclusions We report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.

Background Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied. Methods We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers. Results In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.

Bauhinia coccinea is a tropical woody plant widely distributed in Vietnam and Unnan in southern China. Although many studies have shown the biological activities of extracts from various other species in the genus, no studies have investigated the effects of B. coccinea extracts on biological systems. In the present study, a quantitative analysis of four marker compounds of ethanol extracts of B. coccinea branches (EEBC) was performed using the high performance liquid chromatography (HPLC)-photodiode array (PDA) method. Among gallic acid, (+)-catechin, ellagic acid, and quercitrin contained in EEBC, the most abundant compound was (+)-catechin (18.736 mg/g). In addition, we investigated the EEBC on neuroprotection, antioxidation, and Alzheimer’s disease (AD) marker molecules, acetylcholinesterase (AChE), and amyloid-β (Aβ). EEBC significantly inhibited hydrogen peroxide (H2O2)-induced cell death in a HT22 neuronal cell line and increased 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 2,2-diphenyl-1-picrylhydrazyl scavenging activity markedly. EEBC also inhibited AChE and Aβ aggregation. Among the four compounds, gallic acid exhibited strong inhibitory effects against AChE activation. In the Aβ aggregation assay, the four marker compounds exhibited inhibitory effects lower than 30%. According to the results, EEBC could exert anti-AChE activation and Aβ aggregation activities based on the interactive effects of the marker compounds. Our findings suggest that EEBC are sources of therapeutic candidates for application in the development of AD medication based on AChE and Aβ dual targeting.

Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of “out of North America” migration in the biogeographic history of the Northern Hemisphere.

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This study investigated the effects of the n-BuOH soluble fraction of Polygoni Cuspidati 80% ethanol extract (POCU1b) on high-fat diet (HFD)-induced obesity, non-alcoholic fatty liver (NAFL), and insulin resistance (IR) to find a safe and more effective agent. HPLC profiling of POCU1b identified seven marker compounds. POCU1b increased glycerol release, cyclic adenosine monophosphate (cAMP) level, and inhibited phosphodiesterase (PDE) activity. Seven weeks of POCU1b treatment decreased body weight gain, weight and adipocyte size in fat tissues, serum lipids, and triglyceride and lipid droplets in the livers of HFD-fed rats. POCU1b improved blood glucose, insulin sensitivity, and impaired insulin secretion in the pancreas. Further, POCU1b ameliorated adiponectin, leptin, IL-6 and TNF-α levels, increased AMPK and p-ACC expression, activated CPT-1 activity, and suppressed FAS mRNA, SOCS-3 protein expression, and NF-κB DNA-binding activity. When compared with the Xenical®-treated group, a positive group, the action of POCU1b on body weight was more effective than that of Xenical. POCU1b did not show side effects, such as oily spotting and loss of appetite. These results suggest that POCU1b possesses therapeutic or preventive potential for obesity, NAFL and IR via inhibitions of pancreatic lipase and cAMP-dependent PDE activity, AMPK activation, and SOCS-3 suppression, without oily spotting and loss of appetite.

Elaeagnus glabra f. oxyphylla (Elaeagnaceae) is a small evergreen tree with narrow lanceolate leaves that is native to Korea. In this work, we studied the chemical composition of E. glabra f. oxyphylla branches (EGFOB) for the first time. Additionally, we evaluated the effects of the ethanol extract of EGFOB and each of its chemical components on key mediators of Alzheimer’s disease (AD), namely, amyloid-β (Aβ) aggregation and oxidative stress. The ethanol extract of EGFOB decreased Aβ aggregation (IC50 = 32.01 µg/mL) and the levels of the oxidative free radicals 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) (IC50 = 11.35 and 12.32 µg/mL, respectively). Sixteen compounds were isolated from EGFOB. Among them, procyanidin B3 (8), procyanidin B4 (9), and helichrysoside (13) significantly inhibited Aβ aggregation (IC50 = 14.59, 32.64, and 44.45 μM, respectively), indicating their potential as bioactive compounds to control Aβ aggregation. Furthermore, these compounds markedly enhanced in vitro scavenging activity against ABTS (IC50 = 3.21–4.61 µM). In the DPPH test, they showed lower scavenging activity than in the ABTS test (IC50 ≥ 54.88 µM). Thus, these results suggest that EGFOB and specifically compounds 8, 9, and 13 may be beneficial in AD prevention and treatment through their antioxidant and anti-Aβ aggregation activities.

The accumulation and formation of advanced glycation end products (AGEs) are related to diabetes and age-related disease. Osteomeles schwerinae C. K. Schneid. (Rosaceae, OSSC) is used traditionally for the treatment of various diseases in Asia. Previous studies have shown that OSSC elicits preventive effects in an in vivo model of diabetes. This study was to evaluate the antiapoptotic effects of dried leaves and twigs of OSSC extract and its major compounds in ARPE-19 cells—spontaneously arising human retinal pigment epithelial cells—under diabetic conditions. To examine the effects of an OSSC extract and its active compounds (acetylvitexin, hyperoside and quercitrin) on apoptosis in methylglyoxal (MG, the active precursor in the formation of AGEs)-treated ARPE-19 cells and the mechanism by which these effects occur, apoptosis was measured using flow cytometry analysis. Protein expression levels of phospho-p53 (p-p53), Bax and Bcl-2 were determined by western blot analyses. The OSSC extract inhibited apoptosis in MG-treated ARPE-19 cells in a dose-dependent manner. The major compounds also reduced the rate of apoptosis. Both the extract and major compounds also inhibited the expression of p-p53 and Bax and increased the levels of Bcl-2 that had been previously reduced by MG treatment. The OSSC extract (0.1 μg/mL) and its major compounds (0.01 μM) attenuated apoptosis in ARPE-19 cells under toxic diabetic conditions by downregulating of expression of p-p53 and Bax. OSSC may serve as an alternative therapy to retard the development of diabetic retinopathy.

The green alga Tetraselmis striata is regarded as a suitable candidate microalga for bio-diesel production. Recently, T. striata was cultured near Yeonghueung Island, Korea, in a “marine culturing field”; however, its environmental impacts are not yet studied. We estimated the amount of dissolved organic carbon (DOC) released from T. striata cultivation in the marine culturing field, and we investigated the changes in bacterial composition. Then, we designed and installed a mesocosm for further understanding. From the mesocosm results, the DOC released from the cultivation of T. striata led to changes in bacterial communities, disturbance of the microbial food web structure, rapid depletion of nutrients, and a decrease in dissolved oxygen (DO) and pH. Our novel work demonstrates that large amounts of DOC secreted by large-scale microalgal cultures such as that of T. striata can potentially have a significant impact on the structure and function of the surrounding microbial ecosystem.

Tribe Forsythieae (Oleaceae), containing two genera (Abeliophyllum and Forsythia) and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 (cyc2) DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe. The chloroplast genomes of the 11 Forsythieae species are highly conserved, except for a deletion of about 400 bp in the accD–psaI region detected only in Abeliophyllum. Within Forsythieae species, analysis of repetitive sequences revealed a total of 51 repeats comprising 26 forward repeats, 22 palindromic repeats, and 3 reverse repeats. Of those, 19 repeats were common and 32 were unique to one or more Forsythieae species. Our phylogenetic analyses supported the monophyly of Forsythia and its sister group is Abeliophyllum using the concatenated dataset of 78 chloroplast genes. Within Forsythia, Forsythia likiangensis and F. giraldiana were basal lineages followed by F. europaea; the three species are characterized by minutely serrate or entire leaf margins. The remaining species, which are distributed in East Asia, formed two major clades. One clade included F. ovata, F. velutina, and F. japonica; they are morphologically supported by broadly ovate leaves. Another clade of F. suspensa, F. saxatilis, F. viridissima, and F. koreana characterized by lanceolate leaves (except F. suspensa which have broad ovate leaves). Although cyc2 phylogeny is largely congruent to chloroplast genome phylogeny, we find the discordance between two phylogenies in the position of F. ovata suggesting that introgression of the chloroplast genome from one species into the nuclear background of another by interspecific hybridization in East Asian Forsythia species. Molecular dating and biogeographic reconstructions suggest an origin of the Forsythieae species in East China in the Miocene. Distribution patterns in Forsythia indicated that the species were radially differentiated from East China, and the speciation of the European F. europaea was the result of both vicariance and dispersal in the late Miocene to Pliocene.

The complete chloroplast genome of Centaurea maculosa (Asteraceae) was presented in this article. The genome size is 152,518 bp in length, with 43.1% of GC content. It consists of a large single-copy (LSC) region (83,959 bp) and a small single-copy region (SSC) (18,487 bp) which were separated by two inverted repeat (IRs) regions (25,218 bp). The complete chloroplast genome contains 111 unique genes, including 80 coding genes, 4 rRNA genes, and 27 tRNA genes.

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore “hot spots” for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections (Veratrum and Fuscoveratrum) of Veratrum. Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3. Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

We aimed to investigate the therapeutic effects of an Elaeagnus glabra f. oxyphylla (EGFO) ethanol extract in mice with scopolamine-induced memory dysfunction. Fifty male mice were randomly divided into a normal control group, a scopolamine-treated group, a scopolamine and EGFO extract-treated group, and a scopolamine and tacrine-treated group. EGFO (50 or 100 mg/kg/day) was received for 21 days. Step-through passive avoidance and Y-maze tests were performed to examine the effects of treatment on learning and memory impairments. Acetylcholine (Ach) levels and acetylcholinesterase (AchE) activity were measured via an enzyme-linked immunosorbent assay (ELISA). Levels of choline acetyltransferase (ChAT), nerve growth factor (NGF), cAMP response element-binding protein (CREB), and apoptosis-related protein expression were determined via Western blot analysis. EGFO pretreatment significantly attenuated scopolamine-induced memory impairments, relative to findings observed in the scopolamine-treated group. Levels of cholinergic factors in the brain tissues were markedly attenuated in the scopolamine-treated group. EGFO treatment also attenuated neural apoptosis in scopolamine-treated mice by decreasing the expression of apoptosis-related proteins such as Bax, Bcl2, cleaved caspase-3, and TUNEL staining. These results suggest that EGFO improves memory and cognition in a mouse model of memory impairment by restoring cholinergic and anti-apoptotic activity, possibly via activation of CREB/NGF signaling.

Retinal apoptosis plays a critical role in the progression of diabetic retinopathy (DR), a common diabetic complication. Currently, the tight control of blood glucose levels is the standard approach to prevent or delay the progression of DR. However, prevalence of DR among diabetic patients remains high. Focusing on natural nutrients or herbal medicines that can prevent or delay the onset of diabetic complications, we administered an ethanol extract of the aerial portion of Osteomeles schwerinae (OSSCE), a Chinese herbal medicine, over a period of 17 weeks to spontaneously diabetic Torii (SDT) rats. OSSCE was found to ameliorate retinal apoptosis through the regulation of advanced glycation end product (AGE) accumulation, oxidative stress, and mitochondrial function via the inhibition of NF-κB activity, in turn, through the downregulation of PKCδ, P47phox, and ERK1/2. We further demonstrated in 25 mM glucose-treated human retinal microvascular endothelial cells (HRMECs) that hyperoside (3-O-galactoside-quercetin), quercitrin (3-O-rhamnoside-quercetin), and 2″-O-acetylvitexin (8-C-(2″-O-acetyl-glucoside)-apigenin) were the active components of OSSCE that mediated its pharmacological action. Our results provide evidence that OSSCE is a powerful agent that may directly mediate a delay in the development or disease improvement in patients of DR.

Pollution-induced skin damage results in oxidative stress; cellular toxicity; inflammation; and, ultimately, premature skin aging. Previous studies suggest that the activation of autophagy can protect oxidation-induced cellular damage and aging-like changes in skin. In order to develop new anti-pollution ingredients, this study screened various kinds of natural extracts to measure their autophagy activation efficacy in cultured dermal fibroblast. The stimulation of autophagy flux by the selected extracts was further confirmed both by the expression of proteins associated with the autophagy signals and by electron microscope. Crepidiastrum denticulatum (CD) extract treated cells showed the highest autophagic vacuole formation in the non-cytotoxic range. The phosphorylation of adenosine monophosphate kinase (AMPK), but not the inhibition of mammalian target of rapamycin (mTOR), was observed by CD-extract treatment. Its anti-pollution effects were further evaluated with model compounds, benzo[a]pyrene (BaP) and cadmium chloride (CdCl2), and a CD extract treatment resulted in both the protection of cytotoxicity and a reduction of proinflammatory cytokines. These results suggest that the autophagy activators can be a new protection regimen for anti-pollution. Therefore, CD extract can be used for anti-inflammatory and anti-pollution cosmetic ingredients.

The identification and quantification of Heterosigma akashiwo cysts in sediments by light microscopy can be difficult due to the small size and morphology of the cysts, which are often indistinguishable from those of other types of algae. Quantitative real-time PCR (qPCR) based assays represent a potentially efficient method for quantifying the abundance of H. akashiwo cysts, although standard curves must be based on cyst DNA rather than on vegetative cell DNA due to differences in gene copy number and DNA extraction yield between these two cell types. Furthermore, qPCR on sediment samples can be complicated by the presence of extracellular DNA debris. To solve these problems, we constructed a cyst-based standard curve and developed a simple method for removing DNA debris from sediment samples. This cyst-based standard curve was compared with a standard curve based on vegetative cells, as vegetative cells may have twice the gene copy number of cysts. To remove DNA debris from the sediment, we developed a simple method involving dilution with distilled water and heating at 75°C. A total of 18 sediment samples were used to evaluate this method. Cyst abundance determined using the qPCR assay without DNA debris removal yielded results up to 51-fold greater than with direct counting. By contrast, a highly significant correlation was observed between cyst abundance determined by direct counting and the qPCR assay in conjunction with DNA debris removal (r2 = 0.72, slope = 1.07, p < 0.001). Therefore, this improved qPCR method should be a powerful tool for the accurate quantification of H. akashiwo cysts in sediment samples.

We report here that an ethanol extract of Tetracera scandens, aVietnamese medicinal plant, has anti-HIV activity and possessesstrong inhibitory activity against HIV-1 reverse transcriptase(RTase). Using a MT-4 cell-based assay, we found thatthe T. scandens extract inhibited effectively HIV virus replicationwith an IC50 value in the range of 2.0-2.5 μg/ml whilethe cellular toxicity value (CC50) was more than 40-50 μg/mlconcentration, thus yielding a minimum specificity index of20-fold. Moreover, the anti-HIV efficacy of the T. scandens extractwas determined to be due, in part, to its potent inhibitoryactivity against HIV-1 RTase activity in vitro. The inhibitory activityagainst the RTase was further confirmed by probing viralcDNA production, an intermediate of viral reverse transcription,in virus-infected cells using quantitative DNA-PCRanalysis. Thus, these results suggest that T. scandens can be auseful source for the isolation and development of new anti-HIV-1 inhibitor(s). [BMB reports 2012; 45(3): 165-170]

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.

Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.