Chromosome-level genome assembly of Korean holoparasitic plants, Orobanche coerulescens.

Orobanche coerulescens is a parasitic plant that cannot complete its life cycle without a host and is incapable of photosynthesis. The habitats of O. coerulescens span the coasts of Korea and its volcanic islands, Ulleungdo and Dokdo. Those on the volcanic islands exhibit morphological differences and have distinct hosts compared to those on the peninsula. The family of Orobanchaceae, encompassing both autotrophic and parasitic species, serves as a model for evolutionary studies of parasitic states. However, there are limited genome assemblies for the Orobanche genus. In our study, we produced approximately 100x ONT long reads to construct a chromosome-level genome of O. coerulescens. The resulting assembly has a total size of 3,648 Mb with an N50 value of 195 Mb, and 82.0% of BUSCO genes were identified as complete. Results of the repeat annotation revealed that 86.3% of the genome consisted of repeat elements, and 29,395 protein-coding genes were annotated. This chromosome-level genome will be an important biological resource for conserving biodiversity and further understanding parasitic plants.

Protocol for in vitro co-culture assay for rapid expansion of human T cell acute lymphoblastic leukemia.

T cell acute lymphoblastic leukemia (T-ALL) is a rare but aggressive hematological cancer that occurs primarily in children and adolescents. Here, we present a protocol for in vitro co-culture assay that enables robust expansion of primary T-ALL cells. We describe steps for seeding T-ALL and stromal cells in 3D organoids and subsequent flow analysis to capture the T-ALL cell growth for long-term culture. This protocol provides a valuable platform for in vitro functional studies and drug screenings using patient-derived cells. For complete details on the use and execution of this protocol, please refer to Rivera et al.1.

Reactive control in suicide ideators and attempters: An examination of the congruency sequence effect in cognitive and emotional Simon tasks.

Reactive control is the cognitive ability to adjust thoughts and behaviors when encountering conflict. We investigated how this ability to manage conflict and stress distinguishes suicidal from nonsuicidal individuals. The hypothesis was that suicidal individuals would show poorer reactive control when faced with conflict generated by emotional than neutral stimuli. Hence, individuals with a lifetime history of suicide ideation or attempt and nonsuicidal controls were tested in cognitive and emotional Simon tasks. We examined the congruency sequence effect (CSE) in the Simon tasks as an indication of the efficiency of reactive control in resolving conflict. Whereas controls demonstrated significant CSEs in both tasks, suicide attempters showed a significant CSE in the cognitive task but not in the emotional task. Suicide ideators, on the other hand, displayed marginally significant CSEs in both tasks. Comparing groups with pairwise comparison demonstrated that the difference in CSE was significant only in the emotional task between attempters and controls. Our findings of attempters' inefficiency in adjusting reactive control during the emotional task reflect cognitive inflexibility in coping with conflicting situations during which suicidal individuals become vulnerable to suicide attempts in states of negative emotion.

Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding.

Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.

The effect of colorization on the fetal lung heterogeneity index.

No previous studies have quantitatively assessed the effect of color tones on ultrasound texture analysis techniques. Our objective was to compare heterogeneity index (HI) between fetal lung images captured in grayscale and those same images after conversion to Ice and Sepia. Fetal lung images were obtained during medically indicated ultrasound examinations. We observed that HI is affected by the application of color tones to ultrasound images of the fetal lung. Therefore, for each type of biological tissue and color tone, determination of distinct HI nomograms and cut off points is recommended.

The complete chloroplast genome sequence of Melampyrum koreanum (Orobanchaceae), an endemic and hemi-parasitic herb in Korea.

Melampyrum koreanum K.-J. Kim and S.-M. Yun 2012 (Orobanchaceae) is a hemi-parasitic herb, endemic to Korea. Here, the chloroplast genome of this species is reported. It was found to be 143,865 bp long, with a large single-copy region of 83,133 bp, a small single-copy region of 10,308 bp, and a pair of inverted repeat regions of 25,212 bp each. The chloroplast genome harbors 124 genes, including 79 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Among the identified genes, rpoA and several ndh genes were determined to be pseudogenized due to the stop codon in the middle of the gene. The phylogenetic tree of the family was reconstructed based on 20 protein-coding genes, conserved across studied taxa. As a result, Melampyrum L. 1753 species were found to form a monophyletic group in the family.

Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses.

The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.

Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution.

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

Cross-task congruency sequence effect without the contribution of multiple expectancy.

The confound-minimized cross-task design has been widely used to examine the characteristics of top-down cognitive control underlying the congruency sequence effect (CSE) without feature integration and contingency learning confounds. The present study reanalyzed our previous data obtained with the confound-minimized cross-task design, this time including the preceding congruency repetition type, to examine whether the cross-task CSE is confounded by feature integration from two-back (n-2) trials or multiple expectancies regarding the congruency and the congruency repetition type of the upcoming trial. As a result, the cross-task CSE interacted with the arbitrariness of S-R mapping or response mode regardless of the preceding congruency repetition type, indicating the contribution of top-down control triggered by conflict. Feature integration from n-2 trials, but not multiple expectancies, was found to have a lingering effect on the sequential modulation of the congruency effect between previous and current trials. However, because the influence of feature integration operated in opposite directions depending on the preceding congruency repetition type, the contribution of feature integration to the cross-task CSE can be minimized when the combined datasets of trials following a congruency repetition trial and those following a congruency alternation trial are analyzed. These findings are consistent with recent perspectives on cognitive control, which posit that top-down cognitive control and bottom-up feature integration operate independently to optimize task performance.

Response mode modulates the congruency sequence effect in spatial conflict tasks: evidence from aimed-movement responses.

The present study investigated how response mode determines the specificity of control responsible for the congruency sequence effect (CSE), especially when conflict arises from spatial dimensions. Horizontal and vertical Simon tasks were presented in turn, while response mode (Experiment 1) or task-relevant stimulus dimension (Experiment 2) was manipulated. All responses were made by aimed movements to make the relative salience of the horizontal and vertical dimensions equivalent regardless of response mode. The confound-minimized CSEs were significant only when the two tasks shared the same response mode, which did not vary as a function of task-relevant stimulus dimension. This result suggests that response mode determines the scope of control, as it reconfigures the representations of the task-irrelevant spatial dimensions (i.e., the horizontal and vertical dimensions), which is corroborated by distributional analyses. This response mode-specific control was also consistently found for the horizontal and vertical arrow versions of flanker-compatibility tasks in Experiment 3, in which conflict does not directly arise from the response dimension. Furthermore, the current findings revealed that the CSEs were more evident in movement times than in initiation times, which provides new insight on how control inhibits the response activated by a task-irrelevant stimulus dimension, especially at a motor level.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications.

BACKGROUND: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. RESULTS: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. CONCLUSIONS: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

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.

The complete chloroplast genome sequence of Aristolochia manshuriensis Kom. (Aristolochiaceae).

Aristolochia manshuriensis is a medicinal plant belonging to the family Aristolichiaceae. In this study, complete chloroplast (cp) genome sequence of A. manshuriensis was characterized through de novo assembly with next-generation sequencing data. The cp genome is 160,182 bp long and has a typical quadripartite organization consisting of a large single-copy (LSC), a small single-copy (SSC), and a pair of inverted repeats (IRs). The cp genome harboured 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that A. manshuriensis has close relationship with Aristolochia macrophylla.

Determining the scope of control underlying the congruency sequence effect: roles of stimulus-response mapping and response mode.

Sequential modulation between two task congruencies has been examined to investigate the nature of the cognitive control mechanism underlying the congruency sequence effect (CSE). Previous results regarding what consecutive tasks must have in common to engender the cross-task CSE are inconsistent. The present study examined the roles of stimulus-response (S-R) mappings and response mode as critical factors in determining the scope of control. Two flanker-compatibility tasks having different stimulus and response sets alternated in turn, and the arbitrariness of S-R mappings alone (Experiment 1) or the arbitrariness of stimulus set and the distinctiveness of response modes (Experiment 2) were manipulated. Experiment 1 showed that non-arbitrary S-R mappings engendered a cross-task CSE even when the response modes were different. However, when S-R mappings were arbitrary in Experiment 2, sequential modulation was evident across two tasks only when their response modes were same, irrespective of the arbitrariness of the stimulus set. These results suggest that the arbitrariness of S-R mappings and response mode are salient task features that reconfigure task representation and consequently determine the scope of the control underlying the CSE.

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.

The complete chloroplast genome sequence of Asarum sieboldii Miq. (Aristolochiaceae), a medicinal plant in Korea.

Asarum sieboldii is a medicinal plant belonging to the Aristolochiaceae family. In this study, complete chloroplast genome sequence of A. sieboldii was characterized through de novo assembly with next generation sequencing data. The chloroplast genome is 193,356 bp long and has the stereotypical tripartite organization consisting of large single copy region and a pair of inverted repeats. The genome contains 78 protein-coding genes, 30 rRNA genes, and 4 tRNA genes. Phylogenetic analysis revealed that A. sieboldii has close relationship with Piper coenoclatum (Piperaceae, Piperales).

The complete chloroplast genome of Artemisia hallaisanensis Nakai (Asteraceae), an endemic medicinal herb in Korea.

We determined the complete chloroplast DNA sequence of Artemisia hallaisanensis Nakai, an endemic herbal species distributed on Jeju Island, Korea. The chloroplast DNA is 151,015 bp in length and encodes 4 rRNA, 30 tRNA, and 80 protein-coding genes. Phylogenetic analysis and sequence comparison of protein-coding genes with other Artemisa chloroplast DNAs revealed that the chloroplast genome of A. hallaisanensis is closely related to that of A. capillaris. Additionally, a unique 9 bp deletion in ycf1 gene is specific to A. hallaisanensis.

The complete chloroplast genome of Aconitum chiisanense Nakai (Ranunculaceae).

We determined the complete chloroplast DNA sequence of Aconitum chiisanense Nakai, a rare Aconitum species endemic to Korea. The chloroplast genome is 155 934 bp in length and contains 4 rRNA, 30 tRNA, and 78 protein-coding genes. Phylogenetic analysis revealed that the chloroplast genome of A. chiisanense is closely related to that of A. barbatum var. puberulum. Sequence comparison with other Ranunculaceae chloroplasts identified a unique deletion in the rps16 gene of A. chiisanense chloroplast DNA that can serve as a molecular marker for species identification.

The complete chloroplast genome sequences of Iris sanguinea donn ex Hornem.

The complete chloroplast genome of Iris sanguinea was sequenced newly in this study. The total chloroplast genome size of I. sanguinea was 152 408 bp, its structure and gene contents were well conserved as typical chloroplast characteristics. Large single copy (LSC) and small single copy (SSC) of 82 340 bp and 18 016 bp, respectively, were separated from a pair of inverted repeats (IRA and IRB) of 26 026 bp. A total of 112 genes, i.e. 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, were encoded in the chloroplast genome of I. sanguinea. Overall GC content of I. sanguinea was 36.83%. Phylogenetic analysis with the reported chloroplast genomes revealed that I. sanguinea is most closely related to I. gatesii.

The complete chloroplast genome of a Korean endemic ornamental plant Hosta yingeri S. B. Jones (Asparagaceae).

Hosta yingeri is a perennial herbal ornamental plant belonging to the Asparagaceae family and an endemic species distributed in islands of Korea. In this study, complete chloroplast genome sequence of H. yingeri was characterized through de novo assembly with next generation sequencing data. The chloroplast genome is 156,756 bp in length and contains four rRNA genes, 30 tRNA genes, and 77 protein-coding genes. Phylogenetic analysis demonstrated a close relationship of H. yingeri with other species belonging to the subfamily Agavoideae in Asparagaceae.