Genome-wide functional analysis of pathogenicity genes in the rice blast fungus.

Rapid translation of genome sequences into meaningful biological information hinges on the integration of multiple experimental and informatics methods into a cohesive platform. Despite the explosion in the number of genome sequences available, such a platform does not exist for filamentous fungi. Here we present the development and application of a functional genomics and informatics platform for a model plant pathogenic fungus, Magnaporthe oryzae. In total, we produced 21,070 mutants through large-scale insertional mutagenesis using Agrobacterium tumefaciens-mediated transformation. We used a high-throughput phenotype screening pipeline to detect disruption of seven phenotypes encompassing the fungal life cycle and identified the mutated gene and the nature of mutation for each mutant. Comparative analysis of phenotypes and genotypes of the mutants uncovered 202 new pathogenicity loci. Our findings demonstrate the effectiveness of our platform and provide new insights on the molecular basis of fungal pathogenesis. Our approach promises comprehensive functional genomics in filamentous fungi and beyond.

Bidirectional-genetics platform, a dual-purpose mutagenesis strategy for filamentous fungi.

Rapidly increasing fungal genome sequences call for efficient ways of generating mutants to translate quickly gene sequences into their functions. A reverse genetic strategy via targeted gene replacement (TGR) has been inefficient for many filamentous fungi due to dominant production of undesirable ectopic transformants. Although large-scale random insertional mutagenesis via transformation (i.e., forward genetics) facilitates high-throughput uncovering of novel genes of interest, generating a huge number of transformants, which is necessary to ensure the likelihood of mutagenizing most genes, is time-consuming. We propose a new strategy, entitled the Bidirectional-Genetics (BiG) platform, which combines both forward and reverse genetic strategies by recycling ectopic transformants derived from TGR as a source for random insertional mutants. The BiG platform was evaluated using the rice blast fungus Magnaporthe oryzae as a model. Over 10% of >1,000 M. oryzae ectopic transformants, generated during disruption of specific genes, displayed abnormality in vegetative growth, pigmentation, and/or asexual reproduction. In this pool of putative mutants, we isolated insertional mutants with mutations in three genes involved in histidine biosynthesis (MoHIS5), vegetative growth (MoVPS74), or conidiophore formation (MoFRQ) (where "Mo" indicates "M. oryzae"), supporting the utility of this platform for systematic gene function studies.

First Report of Endemic Frog Virus 3 (FV3)-like Ranaviruses in the Korean Clawed Salamander (Onychodactylus koreanus) in Asia.

Frog virus 3 (FV3) in the genus Ranavirus of the family Iridoviridae causes mass mortality in both anurans and urodeles worldwide; however, the phylogenetic origin of FV3-like ranaviruses is not well established. In Asia, three FV3-like ranaviruses have been reported in farmed populations of amphibians and reptiles. Here, we report the first case of endemic FV3-like ranavirus infections in the Korean clawed salamander Onychodactylus koreanus, caught in wild mountain streams in the Republic of Korea (ROK), through whole-genome sequencing and phylogenetic analysis. Two isolated FV3-like ranaviruses (Onychodactylus koreanus ranavirus, OKRV1 and 2) showed high similarity with the Rana grylio virus (RGV, 91.5%) and Rana nigromaculata ranavirus (RNRV, 92.2%) but relatively low similarity with the soft-shelled turtle iridovirus (STIV, 84.2%) in open reading frame (ORF) comparisons. OKRV1 and 2 formed a monophyletic clade with previously known Asian FV3-like ranaviruses, a sister group of the New World FV3-like ranavirus clade. Our results suggest that OKRV1 and 2 are FV3-like ranaviruses endemic to the ROK, and RGV and RNRV might also be endemic strains in China, unlike previous speculation. Our data have great implications for the study of the phylogeny and spreading routes of FV3-like ranaviruses and suggest the need for additional detection and analysis of FV3-like ranaviruses in wild populations in Asian countries.

Identifying the source rookery of green turtles (Chelonia mydas) found in feeding grounds around the Korean Peninsula.

Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation.

Monolayer, open-mesh, pristine PEDOT:PSS-based conformal brain implants for fully MRI-compatible neural interfaces.

Understanding brain function is essential for advancing our comprehension of human cognition, behavior, and neurological disorders. Magnetic resonance imaging (MRI) stands out as a powerful tool for exploring brain function, providing detailed insights into its structure and physiology. Combining MRI technology with electrophysiological recording system can enhance the comprehension of brain functionality through synergistic effects. However, the integration of neural implants with MRI technology presents challenges because of its strong electromagnetic (EM) energy during MRI scans. Therefore, MRI-compatible neural implants should facilitate detailed investigation of neural activities and brain functions in real-time in high resolution, without compromising patient safety and imaging quality. Here, we introduce the fully MRI-compatible monolayer open-mesh pristine PEDOT:PSS neural interface. This approach addresses the challenges encountered while using traditional metal-based electrodes in the MRI environment such as induced heat or imaging artifacts. PEDOT:PSS has a diamagnetic property with low electrical conductivity and negative magnetic susceptibility similar to human tissues. Furthermore, by adopting the optimized open-mesh structure, the induced currents generated by EM energy are significantly diminished, leading to optimized MRI compatibility. Through simulations and experiments, our PEDOT:PSS-based open-mesh electrodes showed improved performance in reducing heat generation and eliminating imaging artifacts in an MRI environment. The electrophysiological recording capability was also validated by measuring the local field potential (LFP) from the somatosensory cortex with an in vivo experiment. The development of neural implants with maximized MRI compatibility indicates the possibility of potential tools for future neural diagnostics.

Bionic artificial skin with a fully implantable wireless tactile sensory system for wound healing and restoring skin tactile function.

Tactile function is essential for human life as it enables us to recognize texture and respond to external stimuli, including potential threats with sharp objects that may result in punctures or lacerations. Severe skin damage caused by severe burns, skin cancer, chemical accidents, and industrial accidents damage the structure of the skin tissue as well as the nerve system, resulting in permanent tactile sensory dysfunction, which significantly impacts an individual's daily life. Here, we introduce a fully-implantable wireless powered tactile sensory system embedded artificial skin (WTSA), with stable operation, to restore permanently damaged tactile function and promote wound healing for regenerating severely damaged skin. The fabricated WTSA facilitates (i) replacement of severely damaged tactile sensory with broad biocompatibility, (ii) promoting of skin wound healing and regeneration through collagen and fibrin-based artificial skin (CFAS), and (iii) minimization of foreign body reaction via hydrogel coating on neural interface electrodes. Furthermore, the WTSA shows a stable operation as a sensory system as evidenced by the quantitative analysis of leg movement angle and electromyogram (EMG) signals in response to varying intensities of applied pressures.

HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis.

To cope with a lifetime of exposure to a variety of pathogens, plants have developed exquisite and refined defense mechanisms that vary depending on the type of attacking pathogen. Defense-associated transcriptional reprogramming is a central part of plant defense mechanisms. Chromatin modification has recently been shown to be another layer of regulation for plant defense mechanisms. Here, we show that the RPD3/HDA1-class histone deacetylase HDA19 is involved in the repression of salicylic acid (SA)-mediated defense responses in Arabidopsis. Loss of HDA19 activity increased SA content and increased the expression of a group of genes required for accumulation of SA as well as pathogenesis related (PR) genes, resulting in enhanced resistance to Pseudomonas syringae. We found that HDA19 directly associates with and deacetylates histones at the PR1 and PR2 promoters. Thus, our study shows that HDA19, by modifying chromatin to a repressive state, ensures low basal expression of defense genes, such as PR1, under unchallenged conditions, as well as their proper induction without overstimulation during defense responses to pathogen attacks. Thus, the role of HDA19 might be critical in preventing unnecessary activation and self-destructive overstimulation of defense responses, allowing successful growth and development.

Distribution and habitat assessments of the Slender racer, Orientocoluber spinalis, for the registration of nationally endangered species in the Republic of Korea.

Conservation assessments are essential for preserving biodiversity. However, many reptile species have not been evaluated owing to data deficiencies. The Slender racer (Orientocoluber spinalis) is threatened in four out of six inhabiting countries. However, despite its apparent rarity and data deficiency, the International Union for Conservation of Nature (IUCN) has classified it as a Least Concern. In this study, we combined field surveys, habitat analysis, and ecological niche models (ENMs) to identify the critical habitat characteristics of O. spinalis, evaluate its distribution status in the Republic of Korea, and register it as a nationally endangered species. Across the country, we found a few small populations on the mainland but large populations on the islands. Orientocoluber spinalis is mainly found in low-altitude ecotone habitats between grasslands and forests. Based on previous genetic and climatic studies, we propose designating it as an endangered species to conserve this species in protected areas such as national parks, and its non-isolated mainland populations can be preserved as source populations.

A wireless, solar-powered, optoelectronic system for spatial restriction-free long-term optogenetic neuromodulations.

Numerous wireless optogenetic systems have been reported for practical tether-free optogenetics in freely moving animals. However, most devices rely on battery-powered or coil-powered systems requiring periodic battery replacement or bulky, high-cost charging equipment with delicate antenna design. This leads to spatiotemporal constraints, such as limited experimental duration due to battery life or animals' restricted movement within specific areas to maintain wireless power transmission. In this study, we present a wireless, solar-powered, flexible optoelectronic device for neuromodulation of the complete freely behaving subject. This device provides chronic operation without battery replacement or other external settings including impedance matching technique and radio frequency generators. Our device uses high-efficiency, thin InGaP/GaAs tandem flexible photovoltaics to harvest energy from various light sources, which powers Bluetooth system to facilitate long-term, on-demand use. Observation of sustained locomotion behaviors for a month in mice via secondary motor cortex area stimulation demonstrates the notable capabilities of our device, highlighting its potential for space-free neuromodulating applications.

Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae.

The appropriate development of conidia and appressoria is critical in the disease cycle of many fungal pathogens, including Magnaporthe oryzae. A total of eight genes (MoHOX1 to MoHOX8) encoding putative homeobox transcription factors (TFs) were identified from the M. oryzae genome. Knockout mutants for each MoHOX gene were obtained via homology-dependent gene replacement. Two mutants, DeltaMohox3 and DeltaMohox5, exhibited no difference to wild-type in growth, conidiation, conidium size, conidial germination, appressorium formation, and pathogenicity. However, the DeltaMohox1 showed a dramatic reduction in hyphal growth and increase in melanin pigmentation, compared to those in wild-type. DeltaMohox4 and DeltaMohox6 showed significantly reduced conidium size and hyphal growth, respectively. DeltaMohox8 formed normal appressoria, but failed in pathogenicity, probably due to defects in the development of penetration peg and invasive growth. It is most notable that asexual reproduction was completely abolished in DeltaMohox2, in which no conidia formed. DeltaMohox2 was still pathogenic through hypha-driven appressoria in a manner similar to that of the wild-type. However, DeltaMohox7 was unable to form appressoria either on conidial germ tubes, or at hyphal tips, being non-pathogenic. These factors indicate that M. oryzae is able to cause foliar disease via hyphal appressorium-mediated penetration, and MoHOX7 is mutually required to drive appressorium formation from hyphae and germ tubes. Transcriptional analyses suggest that the functioning of M. oryzae homeobox TFs is mediated through the regulation of gene expression and is affected by cAMP and Ca(2+) signaling and/or MAPK pathways. The divergent roles of this gene set may help reveal how the genome and regulatory pathways evolved within the rice blast pathogen and close relatives.

Prevalence of Ranavirus Infection in Three Anuran Species across South Korea.

To cope with amphibian die-offs caused by ranavirus, it is important to know the underlying ranavirus prevalence in a region. We studied the ranavirus prevalence in tadpoles of two native and one introduced anuran species inhabiting agricultural and surrounding areas at 49 locations across eight provinces of South Korea by applying qPCR. The local ranavirus prevalence and the individual infection rates at infected locations were 32.6% and 16.1%, respectively, for Dryophytes japonicus (Japanese tree frog); 25.6% and 26.1% for Pelophylax nigromaculatus (Black-spotted pond frog); and 30.5% and 50.0% for Lithobates catesbeianus (American bullfrog). The individual infection rate of L. catesbeianus was significantly greater than that of D. japonicus. The individual infection rate of P. nigromaculatus was related to the site-specific precipitation and air temperature. The individual infection rate gradually increased from Gosner development stage 39, and intermittent infection was confirmed in the early and middle developmental stages. Our results show that ranavirus is widespread among wild amphibians living in agricultural areas of South Korea, and mass die-offs by ranavirus could occur at any time.

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA.

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Past, present, and future predictions on the suitable habitat of the Slender racer (Orientocoluber spinalis) using species distribution models.

Species distribution models (SDMs) across past, present, and future timelines provide insights into the current distribution of these species and their reaction to climate change. Specifically, if a species is threatened or not well-known, the information may be critical to understand that species. In this study, we computed SDMs for Orientocoluber spinalis, a monotypic snake genus found in central and northeast Asia, across the past (last interglacial, last glacial maximum, and mid-Holocene), present, and future (2070s). The goal of the study was to understand the shifts in distribution across time, and the climatic factors primarily affecting the distribution of the species. We found the suitable habitat of O. spinalis to be persistently located in cold-dry winter and hot summer climatic areas where annual mean temperature, isothermality, and annual mean precipitation were important for suitable habitat conditions. Since the last glacial maximum, the suitable habitat of the species has consistently shifted northward. Despite the increase in suitable habitat, the rapid alterations in weather regimes because of climate change in the near future are likely to greatly threaten the southern populations of O. spinalis, especially in South Korea and China. To cope with such potential future threats, understanding the ecological requirements of the species and developing conservation plans are urgently needed.

Movement Patterns of Juvenile Loggerhead Turtles (Caretta caretta L. 1758) and Green Turtles (Chelonia mydas L. 1758) Hatched in Captivity and Released in the Korean Waters.

With most sea turtle populations declining, activities to conserve their habitat and nesting grounds and restore their populations are being implemented worldwide. To preserve the Northwestern Pacific populations, the National Marine Biodiversity Institute of Korea has been releasing artificially propagated sea turtles, but whether these individuals join the wild population remains unknown. The present study aimed to determine the movement patterns of artificially propagated juvenile loggerhead (Caretta caretta) and green (Chelonia mydas) turtles fitted with satellite transmitters on their carapaces and released in the waters of Jeju or Yeosu, Republic of Korea, between August 2018 and April 2022. Loggerheads traveled northward to the East Sea, whereas green turtles moved west or southwest. Two 36-month-old and two 48-month-old loggerheads moved toward their potential nursery grounds and toward their feeding grounds, respectively. Three green turtles with a curved carapace length (CCL) of <40 cm moved toward their nursery or feeding grounds, while three individuals (CCL > 45 cm) moved toward their inshore foraging areas. The travel paths were closely related to the direction of local sea currents. Our results implied that releasing artificially propagated sea turtles, considering their age and CCL, can positively contribute to the conservation of Northwestern Pacific populations.

The cell cycle gene MoCDC15 regulates hyphal growth, asexual development and plant infection in the rice blast pathogen Magnaporthe oryzae.

Rice blast, caused by the pathogen Magnaporthe oryzae, is a serious hindrance to rice production and has emerged as an important model for the characterization of molecular mechanisms relevant to pathogenic development in plants. Similar to other pathogenic fungi, conidiation plays a central role in initiation of M.oryzae infection and spread over a large area. However, relatively little is known regarding the molecular mechanisms that underlie conidiation in M. oryzae. To better characterize these mechanisms, we identified a conidiation-defective mutant, ATMT0225B6 (MoCDC15(T-DNA)), in which a T-DNA insertion disrupted a gene that encodes a homolog of fission yeast cdc15, and generated a second strain containing a disruption in the same allele (ΔMoCDC15(T-DNA)). The cdc15 gene has been shown to act as a coordinator of the cell cycle in yeast. Functional analysis of the MoCDC15(T-DNA) and ΔMoCDC15(T-DNA) mutants revealed that MoCDC15 is required for conidiation, preinfection development and pathogenicity in M. oryzae. Conidia from these mutants were viable, but failed to adhere to hydrophobic surface, a crucial step required for subsequent pathogenic development. All phenotypic defects observed in mutants were rescued in a strain complemented with wild type MoCDC15. Together, these data indicate that MoCDC15 functions as a coordinator of several biological processes important for pathogenic development in M. oryzae.

Genetic and molecular characterization of a blue light photoreceptor MGWC-1 in Magnaporth oryzae.

Three key factors involved in successful plant disease development include the presence of a susceptible host, a virulent pathogen, and a disease-conducive environment. Our understanding of how environmental factors influence disease-conducive or disease-suppressive conditions, and how a pathogen advantageously capitalizes on them, is quite limited. Utilizing the model pathosystem Magnaporthe oryzae-Oryza sativa, we found a significant light-dependent disease suppression. Our genetic data suggest that the blue-light receptor MGWC-1 in M. oryzae is involved in light-dependent disease suppression during the dark-phase (disease-conducive light condition) immediately after pathogen-host contact. Sensing "darkness" is accomplished by MGWC-1, a blue-light receptor in M. oryzae. To explore the potential molecular mechanisms of light-dependent disease suppression we performed a genome-wide microarray experiment and identified several groups of gene families that are differentially regulated during the light-to-dark transition. Our genetic and molecular data provide insights into how a fungal pathogen utilizes ambient light signals for successful disease development.

CFGP: a web-based, comparative fungal genomics platform.

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

Writing styles of a Korean sample by age: an exploratory study.

This descriptive study concerned whether language use differs across age groups of Korean participants. Language use by Koreans in their 20s, 40s, and 60s were compared using the Korean Linguistic Inquiry and Word Count. Analysis showed that Koreans in their 60s used as many phrases and morphemes per sentence as younger people, which reflects similar complexity of language. In addition, those in their 40s showed the strongest use of words related to emotion, cognition, work, and leisure. These results show interesting differences from studies conducted with Western subjects.

The complete mitochondrial genome of a yellow-bellied sea snake (Hydrophis platurus) (Squamata, Elapidae).

In this study, we provide the first report of the complete mitochondrial genomic sequencing of a yellow-bellied sea snake (Hydrophis platurus) that has the broadest distribution range of all Squamata species. The mitogenome length was 18,101 bp and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 3 non-coding regions. The sequence presented could be very useful for further phylogenetic and evolutionary studies.

Genetic diversity and inferred dispersal history of the Schlegel's Japanese Gecko (Gekko japonicus) in Northeast Asia based on population genetic analyses and paleo-species distribution modelling.

To understand the genetic diversity and dispersal history of Schlegel's Japanese gecko (Gekko japonicus), we performed genetic analyses and paleo-species distributional modelling. For the genetic analysis, we analyzed mitochondrial DNA (mtDNA) (cytochrome b [Cytb] and NADH dehydrogenase 2 [ND2]) and seven microsatellite loci of 353 individuals from 11 populations (2 east coast China, 4 west and central coast Japan and 5 Korea). For the paleo-species distribution modelling, we used 432 occurrence data points (125 China, 291 Japan and 16 Korea) over the Pleistocene and Holocene. China is inferred to be the source population, which had higher genetic diversity (mtDNA) and more private alleles (mtDNA) compared to Japanese and Korean populations. Differences between the three counties were very small in the mtDNA haplotype network despite some genetic structure among the three countries. Microsatellite analysis inferred that genetic exchange has actively occurred among the Chinese, Japanese and Korean populations. Suitable habitats in Japan should have been plentiful by the mid-Holocene, but have only recently become available in Korea. These results suggest that dispersal of G. japonicus occurred after the Holocene warming from the east coast of China to the west and central coasts of Japan and Korea, and gene flow is actively occurring among the three countries.