First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae).

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.

Characterization of the complete plastid genome and phylogenetic implication of Micranthes octopetala (Nakai) Y.I.Kim & Y.D.Kim (Saxifragaceae), endemic to Korea.

Micranthes octopetala (Nakai) Y.I.Kim & Y.D. Kim et al. 2015, which belongs to the family Saxifragaceae, is a perennial herb endemic to Korea. M. octopetala was originally treated as a synonym of M. manchuriensis. However, in 2015, molecular phylogenetic analysis confirmed that M. octopetala is an independent species. In this study, the plastid genome of M. octopetala was sequenced for the first time, and the taxonomic position of this species was identified. The complete plastid genome of M. octopetala has a total length of 149 751 bp (large single copy: 83 083 bp; small single copy: 17 196 bp; inverted repeat: 24 736 bp), containing 130 genes, including 79 CDS, 30 tRNAs, and 4 rRNAs. Moreover, the absence of intron in the rpl2 gene, which is a common feature of Saxifragaceae, was confirmed. Phylogenetic analysis based on 79 protein-coding genes from 21 species revealed that M. octopetala belongs to the genus Micranthes, being a sister to other Micranthes species. The plastid genome of M. octopetala obtained in this study provides fundamental information for future studies on the genus Micranthes.

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.

Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

Machine-learning-assisted analysis of transition metal dichalcogenide thin-film growth.

In situ reflective high-energy electron diffraction (RHEED) is widely used to monitor the surface crystalline state during thin-film growth by molecular beam epitaxy (MBE) and pulsed laser deposition. With the recent development of machine learning (ML), ML-assisted analysis of RHEED videos aids in interpreting the complete RHEED data of oxide thin films. The quantitative analysis of RHEED data allows us to characterize and categorize the growth modes step by step, and extract hidden knowledge of the epitaxial film growth process. In this study, we employed the ML-assisted RHEED analysis method to investigate the growth of 2D thin films of transition metal dichalcogenides (ReSe2) on graphene substrates by MBE. Principal component analysis (PCA) and K-means clustering were used to separate statistically important patterns and visualize the trend of pattern evolution without any notable loss of information. Using the modified PCA, we could monitor the diffraction intensity of solely the ReSe2 layers by filtering out the substrate contribution. These findings demonstrate that ML analysis can be successfully employed to examine and understand the film-growth dynamics of 2D materials. Further, the ML-based method can pave the way for the development of advanced real-time monitoring and autonomous material synthesis techniques.

Characterization of the complete plastid genome of Korean endemic, Ajuga spectabilis Nakai (Lamiaceae).

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.

Complete plastid genome of Lespedeza tricolor (Fabaceae), an endemic shrub in Korea.

Lespedeza tricolor is a species found in the southern province of Korea, thought to be endemic to Korea. The complete plastid genome of this legume was sequenced in this study. DNA from L. tricolor was extracted, sequenced, and assembled into the complete plastid genome. We used 18 species of the family Fabaceae and 77 protein-coding genes to perform phylogenetic analysis. The plastid genome is 149,038 bp in length, with large (82,495 bp) and small (18,889 bp) single-copy regions, separated by a pair of inverted repeat regions (23,827 bp). It contains 83 protein-coding genes, eight rRNAs, 37 tRNAs, and two pseudogenes (rpl22 and infA). Our phylogenetic analysis suggests that the genus Lespedeza is monophyletic and L. tricolor is closely related to L. maritima and L. buergeri. In this study, we identified the phylogenetic position of L. tricolor and provided the data that can be used in various ways in future studies.

First record of the complete chloroplast genome of Syneilesis aconitifolia (Asteraceae).

Syneilesis aconitifolia is an herbaceous perennial of the Asteraceae family native to forests in China, Korea, Japan, and eastern Russia. In Korea, the young leaves of the plant are edible and the extract is known to have antitumor effects. The length of the complete plastome was found to be 150,773 bp, including 130 genes, consisting of 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The assembled plastome showed typical structure and gene content of the angiosperm plastome, which includes two inverted repeats (IR) regions of 24839 bp, a large single copy (LSC) region of 82911 bp, and a small single-copy (SSC) region of 18184 bp. The total G/C content in the S. aconitifolia plastome was 37.5%. The maximum likelihood (ML) phylogenetic tree strongly supports that S. aconitifolia is closely related to the hosts of Ligularia fischeri. This study reports the first complete chloroplast genome of the genus Syneilesis and will contribute to the phylogenetics of the family Asteraceae.

Tuning of Thermoelectric Properties of MoSe2 Thin Films Under Helium Ion Irradiation.

Transition metal dichalcogenides have attracted renewed interest for use as thermoelectric materials owing to their tunable bandgap, moderate Seebeck coefficient, and low thermal conductivity. However, their thermoelectric parameters such as Seebeck coefficient, electrical conductivity, and thermal conductivity are interdependent, which is a drawback. Therefore, it is necessary to find a way to adjust one of these parameters without affecting the other parameters. In this study, we investigated the effect of helium ion irradiation on MoSe2 thin films with the objective of controlling the Seebeck coefficient and electrical conductivity. At the optimal irradiation dose of 1015 cm-2, we observed multiple enhancements of the power factor resulting from an increase in the electrical conductivity, with slight suppression of the Seebeck coefficient. Raman spectroscopy, X-ray diffraction, and transmission electron microscopy analyses revealed that irradiation-induced selenium vacancies played an important role in changing the thermoelectric properties of MoSe2 thin films. These results suggest that helium ion irradiation is a promising method to significantly improve the thermoelectric properties of two-dimensional transition metal dichalcogenides. Effect of He+ irradiation on thermoelectric properties of MoSe2 thin films.

Ultrafast Triggering of Insulator-Metal Transition in Two-Dimensional VSe2.

The transition-metal dichalcogenide VSe2 exhibits an increased charge density wave transition temperature and an emerging insulating phase when thinned to a single layer. Here, we investigate the interplay of electronic and lattice degrees of freedom that underpin these phases in single-layer VSe2 using ultrafast pump-probe photoemission spectroscopy. In the insulating state, we observe a light-induced closure of the energy gap, which we disentangle from the ensuing hot carrier dynamics by fitting a model spectral function to the time-dependent photoemission intensity. This procedure leads to an estimated time scale of 480 fs for the closure of the gap, which suggests that the phase transition in single-layer VSe2 is driven by electron-lattice interactions rather than by Mott-like electronic effects. The ultrafast optical switching of these interactions in SL VSe2 demonstrates the potential for controlling phase transitions in 2D materials with light.

Rolling up MoSe2 Nanomembranes as a Sensitive Tubular Photodetector.

Transition metal dichalcogenides, as a kind of 2D material, are suitable for near-infrared to visible photodetection owing to the bandgaps ranging from 1.0 to 2.0 eV. However, limited light absorption restricts photoresponsivity due to the ultrathin thickness of 2D materials. 3D tubular structures offer a solution to solve the problem because of the light trapping effect which can enhance optical absorption. In this work, thanks to mechanical flexibility of 2D materials, self-rolled-up technology is applied to build up a 3D tubular structure and a tubular photodetector is realized based on the rolled-up molybdenum diselenide microtube. The tubular device is shown to present one order higher photosensitivity compared with planar counterparts. Enhanced optical absorption arising from the multiple reflections inside the tube is the main reason for the increased photocurrent. This tubular device offers a new design for increasing the efficiency of transition metal dichalcogenide-based photodetection and could hold great potential in the field of 3D optoelectronics.

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries.

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.

The complete chloroplast genome sequence of Hydrangea luteovenosa (Hydrangeaceae).

Hydrangea luteovenosa is a member of the family Hydrangeaceae. The complete chloroplast genome sequence of H. luteovenosa was characterized from MiSeq (Illumina Co.) pair-end sequencing data. The chloroplast genome of H. luteovenosa was 157,494 bp in length with a pair of inverted repeats (IRs) (25,126 bp) which were separated by a large single-copy (LSC) (86,596 bp) and a small single-copy regions (SSC) (18,646 bp). It contained 129 genes including 85 protein-coding genes, 36 tRNA genes, and 8 ribosomal RNA genes. The maximum-likelihood phylogenetic analysis with the previously reported chloroplast genomes showed that H. luteovenosa is most closely related to the tribe Hydrangeeae.

Impact of the cation composition on the electrical performance of solution-processed zinc tin oxide thin-film transistors.

This study examined the structural, chemical, and electrical properties of solution-processed (Zn,Sn)O3 (ZTO) films with various Sn/[Zn+Sn] ratios for potential applications to large-area flat panel displays. ZTO films with a Zn-rich composition had a polycrystalline wurtzite structure. On the other hand, the Sn-rich ZTO films exhibited a rutile structure, where the Zn atom was speculated to replace the Sn site, thereby acting as an acceptor. In the intermediate composition regions (Sn/[Zn+Sn] ratio from 0.28 to 0.48), the ZTO films had an amorphous structure, even after annealing at 450 °C. The electrical transport properties and photobias stability of ZTO thin film transistors (TFTs) were also examined according to the Sn/[Zn+Sn] ratio. The optimal transport property of ZTO TFT was observed for the device with an amorphous structure at a Sn/[Zn+Sn] ratio of 0.48. The mobility, threshold voltage, subthreshold swing, and on/off current ratio were 4.3 cm(2)/(V s), 0 V, 0.4 V/decade, and 4.1 × 10(7), respectively. In contrast, the device performance for the ZTO TFTs with either a higher or lower Sn concentration suffered from low mobility and a high off-state current, respectively. The photoelectrical stress measurements showed that the photobias stability of the ZTO TFTs was improved substantially when the ZTO semiconducting films had a lower oxygen vacancy concentration and an amorphous structure. The relevant rationale is discussed based on the phototransition and subsequent migration mechanism from neutral to positively charged oxygen vacancies.