First report of leaf spot caused by Colletotrichum camelliae in mung beans (Vigna radiata (L.) R. Wilczek) in South Korea.

Mung bean (Vigna radiata (L.) R. Wilczek) is a legume with high nutritional and economic value that is cultivated widely across Asia (Kang et al. 2014). In March 2022, a leaf spot disease in mung bean was observed at the Gangneung-Wonju National University Experimental farm (Gangneung, South Korea, 37.77°N, 128.86°E). The affected plants had irregular brown-gray leaf spots, and the bottom of the leaves showed concentric brown-gray rings that eventually progressed to necrotic lesions. Regardless of the cultivar, approximately 30% of the plants in the field were infected. To isolate the pathogen, the affected leaves were surface-sterilized by washing with 70% ethanol for 1 min, followed by washing with 2% NaClO for 2 min, then rinsing with sterile distilled water. We placed 3-mm sized diseased lesions on potato-dextrose agar (PDA), then incubated them at 27 ± 1 °C in the dark for 7 days and we obtained 1 isolate (CC1). The fungus on PDA had white aerial mycelia that became gray toward the center. Single spore cultures were obtained from fungal isolate. Isolated conidia were single celled, hyaline, cylindrical, and measured between 20.75 to 22.07 µm × 5.85 to 6.92 µm (n = 20), similar to other reports of C. camelliae(Wang et al. 2016). Mycelium from the single spore isolate was used for DNA extraction using Exgene™ Plant SV / (GeneAll®, Cat.No. 117-152), and we amplified the ITS region with primers ITS1 + ITS2 and ITS3 + ITS4, a portion of the actin gene with primers ACT-512F + 738R, and a portion of the beta-tubulin gene with primers BT2aF + BT2bR (Carbone et al. 1999; Glass et al. 1995; White et al. 1990). The amplified regions were sequenced by by Macrogen® (Seoul, South Korea). Sequences were deposited under GenBank accession numbers OR523262 (ITS), OR582483 (Actin), and OR566953 (beta-tubulin). MegaBLAST analysis of the ITS1, ITS2, ACT, and TUB regions showed 99% (216/217 bp) similarity with C. camelliae strain HNCS-26 (MK041440.1), 99% (303/305 bp) similarity with C. camelliae strain G3 (ON025203.1), 99% (242/244 bp) similarity with C. camelliae strain FWT41 (MN525820.1), and 99% (456/460 bp) with C. camelliae strain LF152 (KJ955239.1), respectively. To fulfill Koch's postulates, we conducted a pathogenicity teston the mung bean cultivar VC1973A (Seonhwanokdu) grown for four weeks at 25 °C with a 16-h day/8-h night cycle, simulating the field conditions when the symptoms were observed. We tested the pathogenicity on six plants , three control and three infected plants. Using three leaf replicates per plant resulting in total of nine leaves per group. Leaves were first injured using a sterile needle then either sterile 5 mm PDA plugs or plugs with C. camelliae were placed on the leaf for control and infected conditions, respectively. Irregular gray leaf spots were observed on the abaxial and adaxial of the infected leaf after 2 weeks, like the symptoms observed in the field. This was observed only on infected leaves and nowhere else on the plant and the control plants had no infection. We re-isolated the pathogen from diseased leaves and identified it as C. camelliae using the same molecular markers described previously, completing Koch's postulate. To the best of our knowledge, this is the first report of leaf spot caused by C. camelliae in mung bean plants in Korea, previously the fungi was reported to infect tea plants in Korea (Hassan et al. 2023). More studies are required to investigate potentially resistant mung bean varieties to minimize future damage caused by this fungus.

Sophora genomes provide insight into the evolution of alkaloid metabolites along with small-scale gene duplication.

The genus Sophora (Fabaceae) includes medicinal plants that have been used in East Asian countries since antiquity. Sophora flavescens is a perennial herb indigenous to China, India, Japan, Korea, and Russia. Its dried roots have antioxidant, anti-inflammatory, antibacterial, apoptosis-modulating, and antitumor efficacy. The congeneric S. koreensis is endemic to Korea and its genome is less than half the size of that of S. flavescens. Nevertheless, this discrepancy can be used to assemble and validate the S. flavescens genome. A comparative genomic study of the two genomes can disclose the recent evolutionary divergence of the polymorphic phenotypic profiles of these species. Here, we used the PacBio sequencing platform to sequence and assemble the S. koreensis and S. flavescens genomes. We inferred that it was mainly small-scale duplication that occurred in S. flavescens. A KEGG analysis revealed pathways that might regulate the pharmacologically important secondary metabolites in S. flavescens and S. koreensis. The genome assemblies of Sophora spp. could be used in comparative genomics and data mining for various plant natural products.

Analysis of Changes in Sleep Quality and Patterns after Hip Fracture Using Real Evidence of Artificial Intelligence Linked (REAL) Hip Cohort Data.

Background and Objectives: Hip fractures are commonly found in elderly patients, and often result in chronic pain and decreased physical function, as well as worsening of overall health. It is known that early surgical intervention during the acute phase and rehabilitation are important for improving clinical outcomes for these patients. However, the importance of management for improving the quality of life of these patients is becoming more emphasized. Studies on changes in sleep patterns after hip fractures are rare overseas. Therefore, the aim of this study is to investigate the prevalence of sleep disturbance in patients with hip fractures and to analyze the changes in sleep disturbance after surgery by comparing the preoperative and postoperative results. Materials and Methods: During the period from August 2022 to January 2023, patients who underwent surgical treatment for hip fractures and were recruited into the REAL Hip Cohort were selected as research subjects. The sleep survey was conducted using the Pittsburgh Sleep Quality Index (PSQI). The PSQI is composed of 18 questions, each divided into areas of sleep quality, sleep latency, duration, efficiency, disturbance, use of medication, and daytime dysfunction. Each area is scored 0-3 points and the total is 0-21. A score greater than five indicates sleep disorder. The PSQI was surveyed during hospitalization and three months after surgery for post-fracture sleep status. To analyze changes before and after the fracture, paired T-tests and chi-square tests were performed. Results: From August 2022 to January 2023, a total of 40 patients who were recruited into the REAL Hip Cohort responded to the PSQI survey. The average age was 77.4 years and 36 were female. Sleep quality worsened from 0.75 ± 1.0 before surgery to 1.4 ± 1.0 three months after surgery (p = 0.019), and sleep efficiency also worsened from 0.4 ± 0.6 to 1.4 ± 1.0 (p < 0.001). The PSQI increased from an average of 5.2 ± 2.8 before surgery to 8.2 ± 4.2 three months after surgery (p = 0.007), and the number of patients who could be diagnosed with sleep disorders also increased from 12 (40%) to 24 (60%) (p = 0.030). Conclusions: A decline in overall sleep status was observed in patients in a survey on sleep patterns three months after hip fracture. Additional management is needed to improve their sleep patterns.

Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana.

BACKGROUND: Plants have adapted to survive under adverse conditions or exploit favorable conditions in response to their environment as sessile creatures. In a way of plant adaptation, plant hormones have been evolved to efficiently use limited resources. Plant hormones including auxin, jasmonic acid, salicylic acid, and ethylene have been studied to reveal their role in plant adaptation against their environment by phenotypic observation with experimental design such as mutation on hormone receptors and treatment / non-treatment of plant hormones along with other environmental conditions. With the development of Next Generation Sequencing (NGS) technology, it became possible to score the total gene expression of the sampled plants and estimate the degree of effect of plant hormones in gene expression. This allowed us to infer the signaling pathway through plant hormones, which greatly stimulated the study of functional genomics using mutants. Due to the continued development of NGS technology and analytical techniques, many plant hormone-related studies have produced and accumulated NGS-based data, especially RNAseq data have been stored in the sequence read archive represented by NCBI, EBI, and DDBJ. DESCRIPTION: Here, hormone treatment RNAseq data of Arabidopsis (Col0), wild-type genotype, were collected with mock, SA, and MeJA treatments. The genes affected by hormones were identified through a machine learning approach. The degree of expression of the affected gene was quantified, visualized in boxplot using d3 (data-driven-document), and the database was built by Django. CONCLUSION: Using this database, we created a web application ( http://pgl.gnu.ac.kr/hormoneDB/ ) that lists hormone-related or hormone-affected genes and visualizes the boxplot of the gene expression of selected genes. This web application eventually aids the functional genomics researchers who want to gather the cases of the gene responses by the hormones.

Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato.

Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately threefold compared with a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 °C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually and sexually reproducing plants.

Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection.

BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, "Soybean-VCF2Genomes", http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. CONCLUSION: The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.

Drought resistance is mediated by divergent strategies in closely related Brassicaceae.

Droughts cause severe crop losses worldwide and climate change is projected to increase their prevalence in the future. Similar to the situation for many crops, the reference plant Arabidopsis thaliana (Ath) is considered drought-sensitive, whereas, as we demonstrate, its close relatives Arabidopsis lyrata (Aly) and Eutrema salsugineum (Esa) are drought-resistant. To understand the molecular basis for this plasticity we conducted a deep phenotypic, biochemical and transcriptomic comparison using developmentally matched plants. We demonstrate that Aly responds most sensitively to decreasing water availability with early growth reduction, metabolic adaptations and signaling network rewiring. By contrast, Esa is in a constantly prepared mode as evidenced by high basal proline levels, ABA signaling transcripts and late growth responses. The stress-sensitive Ath responds later than Aly and earlier than Esa, although its responses tend to be more extreme. All species detect water scarcity with similar sensitivity; response differences are encoded in downstream signaling and response networks. Moreover, several signaling genes expressed at higher basal levels in both Aly and Esa have been shown to increase water-use efficiency and drought resistance when overexpressed in Ath. Our data demonstrate contrasting strategies of closely related Brassicaceae to achieve drought resistance.

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance.

BACKGROUND: Bacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species. RESULTS: We resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes. CONCLUSIONS: From our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome.

Translational genomics for plant breeding with the genome sequence explosion.

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

Characterization of the complete chloroplast genome of Wolffia arrhiza and comparative genomic analysis with relative Wolffia species.

Lemnoideae, commonly referred to as the duckweed, are aquatic plants found worldwide. Wolffia species are known for their extreme reduction in size and complexity, lacking both roots and leaves, and they hold the distinction of being the smallest plants among angiosperms. Interestingly, it belongs to the Araceae family, despite its apparent morphological differences from land plants in the same family. Traditional morphological methods have limitations in classifying these plants, making molecular-level information essential. The chloroplast genome of Wolffia arrhiza is revealed that a total length of 169,602 bp and a total GC content of 35.78%. It follows the typical quadripartite structure, which includes a large single copy (LSC, 92,172 bp) region, a small single copy (SSC, 13,686 bp) region, and a pair of inverted repeat (IR, 31,872 bp each) regions. There are 131 genes characterized, comprising 86 Protein-Coding Genes, 37 Transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Moreover, 48 simple sequence repeats and 32 long repeat sequences were detected. Comparative analysis between W. arrhiza and six other Lemnoideae species identified 12 hotspots of high nucleotide diversity. In addition, a phylogenetic analysis was performed using 14 species belonging to the Araceae family and one external species as an outgroup. This analysis unveiled W. arrhiza and Wolffia globosa as closely related sister species. Therefore, this research has revealed the complete chloroplast genome data of W. arrhiza, offering a more detailed understanding of its evolutionary position and phylogenetic categorization within the Lemnoideae subfamily.

Assessment of Automated Identification of Phases in Videos of Total Hip Arthroplasty Using Deep Learning Techniques.

Background: As the population ages, the rates of hip diseases and fragility fractures are increasing, making total hip arthroplasty (THA) one of the best methods for treating elderly patients. With the increasing number of THA surgeries and diverse surgical methods, there is a need for standard evaluation protocols. This study aimed to use deep learning algorithms to classify THA videos and evaluate the accuracy of the labelling of these videos. Methods: In our study, we manually annotated 7 phases in THA, including skin incision, broaching, exposure of acetabulum, acetabular reaming, acetabular cup positioning, femoral stem insertion, and skin closure. Within each phase, a second trained annotator marked the beginning and end of instrument usages, such as the skin blade, forceps, Bovie, suction device, suture material, retractor, rasp, femoral stem, acetabular reamer, head trial, and real head. Results: In our study, we utilized YOLOv3 to collect 540 operating images of THA procedures and create a scene annotation model. The results of our study showed relatively high accuracy in the clear classification of surgical techniques such as skin incision and closure, broaching, acetabular reaming, and femoral stem insertion, with a mean average precision (mAP) of 0.75 or higher. Most of the equipment showed good accuracy of mAP 0.7 or higher, except for the suction device, suture material, and retractor. Conclusions: Scene annotation for the instrument and phases in THA using deep learning techniques may provide potentially useful tools for subsequent documentation, assessment of skills, and feedback.

RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis.

Rice, feeding a significant portion of the world, poses unique proteomic challenges critical to agricultural research and global food security. The complexity of the rice proteome, influenced by various genetic and environmental factors, demands specialized analytical approaches for effective study. The central challenges in rice proteomics lie in developing custom methods suited to the unique aspects of rice biology. These include data preprocessing, method selection, and result validation, all of which are essential for advancing rice research. Our aim is to decode these proteomic intricacies to facilitate breakthroughs in strain improvement, disease resistance, and yield optimization, all vital for combating global food insecurity. To achieve this, we have created the RiceProteomeDB (RPDB), a React + Django database, offering a streamlined and comprehensive platform for the analysis of rice proteomics data. RiceProteomeDB (RPDB) simplifies proteomics data management and analysis. It offers features for data organization, preprocessing, method selection, result validation, and data sharing. Researchers can access processed rice proteomics data, conduct analyses, and explore experimental conditions. The user-friendly web interface enhances navigation and interaction. RPDB fosters collaboration by enabling data sharing and proper acknowledgment of sources, contributing to proteomics research and knowledge dissemination. Availability and implementation: Web application: http://riceproteome.plantprofile.net/ . The web application's source code, user's manual, and sample data: https://github.com/dongu7610/Riceproteome .

Genome-wide SNP discovery in mungbean by Illumina HiSeq.

Mungbean [Vigna radiata (L.) Wilczek], a self-pollinated diploid plant with 2n = 22 chromosomes, is an important legume crop with a high-quality amino acid profile. Sequence variation at the whole-genome level was examined by comparing two mungbean cultivars, Sunhwanokdu and Gyeonggijaerae 5, using Illumina HiSeq sequencing data. More than 40 billion bp from both mungbean cultivars were sequenced to a depth of 72×. After de novo assembly of Sunhwanokdu contigs by ABySS 1.3.2 (N50 = 9,958 bp), those longer than 10 kb were aligned with Gyeonggijaerae 5 reads using the Burrows-Wheeler Aligner. SAMTools was used for retrieving single nucleotide polymorphisms (SNPs) between Sunhwanokdu and Gyeonggijaerae 5, defining the lowest and highest depths as 5 and 100, respectively, and the sequence quality as 100. Of the 305,504 single-base changes identified, 40,503 SNPs were considered heterozygous in Gyeonggijaerae 5. Among the remaining 265,001 SNPs, 65.9 % (174,579 cases) were transitions and 34.1 % (90,422 cases) were transversions. For SNP validation, a total of 42 SNPs were chosen among Sunhwanokdu contigs longer than 10 kb and sharing at least 80 % sequence identity with common bean expressed sequence tags as determined with est2genome. Using seven mungbean cultivars from various origins in addition to Sunhwanokdu and Gyeonggijaerae 5, most of the SNPs identified by bioinformatics tools were confirmed by Sanger sequencing. These genome-wide SNP markers could enrich the current molecular resources and might be of value for the construction of a mungbean genetic map and the investigation of genetic diversity.

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.

The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja, the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja. This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max. In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja/G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

SoyDBean: a database for SNPs reconciliation by multiple versions of soybean reference genomes.

Due to the development of sequence technology and decreased cost, many whole genome sequences have been obtained. As a result, extensive genetic variations have been discovered from many populations and germplasms to understand the genetic diversity of soybean (Glycine max [L.] Merr.). However, assessing the quality of variation is essential because the published variants were collected using different bioinformatic methods and parameters. Furthermore, despite the enhanced genome contiguity and more efficient filling of "N" stretches in the new reference genome, there remains a dearth of endeavors to verify the caliber of variations present in it. The primary goal of this research was to discern a dependable set of SNPs that can withstand reconciliation across multiple reference genomes. Additionally, the investigation aimed to reconfirm the variations through the utilization of numerous whole genome sequencing data obtained from publicly available databases. Based on the result, we created datasets that comprised the thoroughly verified SNP coordinates between the reference assemblies. The resulting "SoyDBean" database is now publicly accessible through the following URL: http://soydbean.plantprofile.net/ .

Prevalence of Sarcopenia in Africa: A Systematic Review.

Objective: The world population gradually getting older, age-related sarcopenia is becoming more frequent. Known to be highly prevalent in high income countries, relative data in Africa are still scarce. This review aims to estimate the prevalence of sarcopenia in Africa and its characteristics. Study Design and Setting: A literature search in PubMed, Web of Science, Google Scholar, and Scopus was conducted in October 2022. All studies reporting the prevalence of sarcopenia in Africa within 15 years were included, and we did an assessment of bias with Hoy et al's risk bias assessment tool. The estimated prevalence of sarcopenia was the outcome and we performed secondary analyses by age, gender, and diagnostic criteria. The random effect model was used for the prevalence estimation. The prevalence of sarcopenia and 95% confidence interval (95% CI) were calculated using the inverse-variance method. Results: A total of 17 studies met our eligibility criteria, for a study population of 12,690 participants with 44.3% males and 55.7% females. The overall prevalence of sarcopenia was 25% (95% CI: 19-30%). The prevalence of sarcopenia among 50 years old and older was 23% (95% CI: 17-29%). We had a higher prevalence of sarcopenia among males (30%, %95 IC: 20-39%) than females (29%, %95 IC: 21-36%). The prevalence of sarcopenia was different depending on the diagnosis criteria used. Conclusion: The prevalence of sarcopenia in Africa was relatively high. However, the fact that the majority of included studies were hospital-based studies shows the necessity of further community-based studies in order to have a more accurate representation of the situation in the general population.

Unraveling the maternal and paternal origins of allotetraploid Vigna reflexo-pilosa.

The genomic structures of Vigna hirtella Ridl. and Vigna trinervia (B.Heyne ex Wight & Arn.) Tateishi & Maxted, key ancestral species of the allotetraploid Vigna reflexo-pilosa var. glabra (Roxb.) N.Tomooka & Maxted, remain poorly understood. This study presents a comprehensive genomic comparison of these species to deepen our knowledge of their evolutionary trajectories. By comparing the genomic profiles of V. hirtella and V. trinervia with those of V. reflexo-pilosa, we investigate the complex genomic mechanisms underlying allopolyploid evolution within the genus Vigna. Comparison of the chloroplast genome revealed that V. trinervia is closely related to V. reflexo-pilosa. De novo assembly of the whole genome, followed by synteny analysis and Ks value calculations, confirms that V. trinervia is closely related to the A genome of V. reflexo-pilosa, and V. hirtella to its B genome. Furthermore, the comparative analyses reveal that V. reflexo-pilosa retains residual signatures of a previous polyploidization event, particularly evident in higher gene family copy numbers. Our research provides genomic evidence for polyploidization within the genus Vigna and identifies potential donor species of allotetraploid species using de novo assembly techniques. Given the Southeast Asian distribution of both V. hirtella and V. trinervia, natural hybridization between these species, with V. trinervia as the maternal ancestor and V. hirtella as the paternal donor, seems plausible.

Correlation between Harris hip score and gait analysis through artificial intelligence pose estimation in patients after total hip arthroplasty.

BACKGROUND: Recently, open pose estimation using artificial intelligence (AI) has enabled the analysis of time series of human movements through digital video inputs. Analyzing a person's actual movement as a digitized image would give objectivity in evaluating a person's physical function. In the present study, we investigated the relationship of AI camera-based open pose estimation with Harris Hip Score (HHS) developed for patient-reported outcome (PRO) of hip joint function. METHOD: HHS evaluation and pose estimation using AI camera were performed for a total of 56 patients after total hip arthroplasty in Gyeongsang National University Hospital. Joint angles and gait parameters were analyzed by extracting joint points from time-series data of the patient's movements. A total of 65 parameters were from raw data of the lower extremity. Principal component analysis (PCA) was used to find main parameters. K-means cluster, X-squared test, Random forest, and mean decrease Gini (MDG) graph were also applied. RESULTS: The train model showed 75% prediction accuracy and the test model showed 81.8% reality prediction accuracy in Random forest. "Anklerang_max", "kneeankle_diff", and "anklerang_rl" showed the top 3 Gini importance score in the Mean Decrease Gini (MDG) graph. CONCLUSION: The present study shows that pose estimation data using AI camera is related to HHS by presenting associated gait parameters. In addition, our results suggest that ankle angle associated parameters could be key factors of gait analysis in patients who undergo total hip arthroplasty.

Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean.

BACKGROUND: R genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain. Some NBS-LRR genes in the soybean genome have also been reported to function in disease resistance. In this study, the number of NBS-LRR genes was found to correlate with the number of disease resistance quantitative trait loci (QTL) that flank these genes in each chromosome. NBS-LRR genes co-localized with disease resistance QTL. The study also addressed the functional redundancy of disease resistance on recently duplicated regions that harbor NBS-LRR genes and NBS-LRR gene expression in the bacterial leaf pustule (BLP)-induced soybean transcriptome. RESULTS: A total of 319 genes were determined to be putative NBS-LRR genes in the soybean genome. The number of NBS-LRR genes on each chromosome was highly correlated with the number of disease resistance QTL in the 2-Mb flanking regions of NBS-LRR genes. In addition, the recently duplicated regions contained duplicated NBS-LRR genes and duplicated disease resistance QTL, and possessed either an uneven or even number of NBS-LRR genes on each side. The significant difference in NBS-LRR gene expression between a resistant near-isogenic line (NIL) and a susceptible NIL after inoculation of Xanthomonas axonopodis pv. glycines supports the conjecture that NBS-LRR genes have disease resistance functions in the soybean genome. CONCLUSIONS: The number of NBS-LRR genes and disease resistance QTL in the 2-Mb flanking regions of each chromosome was significantly correlated, and several recently duplicated regions that contain NBS-LRR genes harbored disease resistance QTL for both sides. In addition, NBS-LRR gene expression was significantly different between the BLP-resistant NIL and the BLP-susceptible NIL in response to bacterial infection. From these observations, NBS-LRR genes are suggested to contribute to disease resistance in soybean. Moreover, we propose models for how NBS-LRR genes were duplicated, and apply Ks values for each NBS-LRR gene cluster.

Tracing soybean domestication history: From nucleotide to genome.

Since the genome sequences of wild species may provide key information about the genetic elements involved in speciation and domestication, the undomesticated soybean (Glycine soja Sieb. and Zucc.), a wild relative of the current cultivated soybean (G. max), was sequenced. In contrast to the current hypothesis of soybean domestication, which holds that the current cultivated soybean was domesticated from G. soja, our previous work has suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. In this review, many structural genomic differences between the two genomes are described and a total of 705 genes are identified as structural variations (SVs) between G. max and G. soja. After protein families database of alignments and hidden Markov models IDs and gene ontology terms were assigned, many interesting genes are discussed in detail using four domestication related traits, such as flowering time, transcriptional factors, carbon metabolism and disease resistance. Soybean domestication history is explored by studying these SVs in genes. Analysis of SVs in genes at the population-level may clarify the domestication history of soybean.