Identifying genes within pathways in unannotated genomes with PaGeSearch.

In biological research, the identification and comparison of genes within specific pathways across the genomes of various species are invaluable. However, annotating the entire genome is resource intensive, and sequence similarity searches often yield results that are not actually genes. To address these limitations, we introduce Pathway Gene Search (PaGeSearch), a tool designed to identify genes from predefined lists, especially those in specific pathways, within genomes. The tool uses an initial sequence similarity search to identify relevant genomic regions, followed by targeted gene prediction and neural network-based result filtering. PaGeSearch suggests the regions that are most likely the orthologs of the genes in the query and is designed to be applicable for species within five classes: mammals, fish, birds, eudicotyledons, and Liliopsida. Compared with GeMoMa and miniprot, PaGeSearch generally outperforms in terms of sensitivity and positive predictive value, as well as negative predictive value. Also, the exon coverage of gene models from PaGeSearch is higher compared with those in GeMoMa and miniprot. Although its performance shows increased variability when applied to actual biological pathways, it nonetheless maintains an acceptable level of accuracy. Evaluating PaGeSearch across different assembly levels, chromosome, scaffold, and contig shows minimal variation in outcomes, indicating that PaGeSearch is resilient to variations in assembly quality.

Genomic insights and comparative analysis of Flavobacterium bizetiae HJ-32-4 isolated from soil.

In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.

The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis.

The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.

Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis.

Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.

COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability.

Seasonal changes in day length are perceived by plant photoreceptors and transmitted to the circadian clock to modulate developmental responses such as flowering time. Blue-light-sensing cryptochromes, the E3 ubiquitin-ligase COP1, and clock-associated proteins ELF3 and GI regulate this process, although the regulatory link between them is unclear. Here we present data showing that COP1 acts with ELF3 to mediate day length signaling from CRY2 to GI within the photoperiod flowering pathway. We found that COP1 and ELF3 interact in vivo and show that ELF3 allows COP1 to interact with GI in vivo, leading to GI degradation in planta. Accordingly, mutation of COP1 or ELF3 disturbs the pattern of GI cyclic accumulation. We propose a model in which ELF3 acts as a substrate adaptor, enabling COP1 to modulate light input signal to the circadian clock through targeted destabilization of GI.

Molecular evolution and functional divergence of X-intrinsic protein genes in plants.

X-intrinsic proteins (XIPs) are a novel class of major intrinsic proteins found in diverse organisms. Recently, XIP genes have been reported to be involved in the transport of a wide range of hydrophobic solutes; however, the evolutionary forces driving their structural and functional divergence in plants are poorly understood. In the present study, comprehensive bioinformatics analyses were performed to gain insight into the molecular and evolutionary mechanisms driving this structural and functional diversification. Phylogenetic analyses have revealed the major lineage-specific expansions of XIP genes in plants. Within the eudicots, XIP genes have diverged into Asterid and Rosid-specific phylogenetic lineages and have also undergone several independent duplications during the course of evolution. Investigation of functional divergence at the protein level showed evidence for shifting evolutionary rate and/or altered constraints on the physiochemical properties of specific amino acid sites following gene duplication. Selection pressure analyses suggest that purifying selection is the predominant evolutionary force acting on the XIP gene subfamily, along with episodic positive selection. However, only a few amino acid sites were found to be subjected to such episodic positive selection. Furthermore, protein functional divergence analysis has identified critical amino acid residues, which must be validated by future experimental studies, that could provide new insights into the role of XIPs in transport of a wide range solutes of physiological importance.

High-quality chromosome-level genome assembly of Nicotiana benthamiana.

Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.

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.

Complete genome sequence of Pectobacterium brasiliense strain 21PCA_AGRO2 with antimicrobial resistance isolated from napa cabbage.

We report a complete genome of Pectobacterium brasiliense strain 21PCA_AGRO2 isolated from napa cabbage, in which the genome consists of a circular chromosome comprising 4,919,671 bp with 4,399 coding DNA sequences, 22 rRNA genes, 77 tRNA genes, and 9 noncoding RNA genes.

Construction of the Whole Genome of Brevundimonas sp. Strain NIBR11: An Exploration of Bacteria Isolated from Algae in the Nakdong River.

We report the genome sequence of Brevundimonas sp. strain NIBR11. Strain NIBR11 was isolated from algae collected from the Nakdong River. The assembled contig contains 3,123 coding sequences (CDSs), 6 rRNA genes, 48 tRNA genes, 1,623 genes for hypothetical proteins, and 109 genes for proteins with putative functions.

Complete Genome Sequence of Phenylobacterium Strain NIBR 498073, Isolated from the Sediment of a Tidal Flat.

We report the complete genome sequence of Phenylobacterium sp. strain NIBR 498073. The sample was isolated from sediment from a tidal flat in Incheon, South Korea. The whole genome consists of one circular chromosome of 4,289,989 bp, and annotation using PGAP predicted 4,160 protein coding genes, 47 tRNAs, 6 rRNAs, and 3 noncoding RNAs.

Complete Genome Sequence of Caulobacter sp. (Strain NIBR1757) Isolated from Lake Chungju in South Korea.

Here, we report the complete genome sequence of strain NIBR1757, isolated from the water of Lake Chungju in South Korea. The assembled genome consists of 4,185 coding sequences (CDSs), 6 rRNAs, and 51 tRNAs. Comparative 16S rRNA gene sequence studies and GTDB-Tk analysis show that this strain belongs to the genus Caulobacter.

Complete Genome Sequence of Sphingomonas sp. Strain NIBR02145.

Sphingomonas sp. strain NIBR02145 is a putative chemoheterotrophic strain that was isolated from soil in Wando-gun, Republic of Korea. The NIBR02145 genome was sequenced with PacBio next-generation sequencing technology. The 5,010,245-bp circular genome has a GC content of 66.79% and harbors 4,561 coding sequences, 6 rRNAs, and 52 tRNAs.

Complete genome sequence of a novel species of Brevundimonas (strain NIBR10).

The complete genome sequence of strain NIBR10 was sequenced using PacBio RS II (Pacific Biosciences) sequencing platform. The 4,006,378-bp genome has a G + C content of 66.89% and around 3,832 coding sequences. Genomic data will provide valuable research for natural taxonomy and comparative genomics of the genus Brevundimonas.

Distinctive origin and evolution of endemic thistle of Korean volcanic island: Structural organization and phylogenetic relationships with complete chloroplast genome.

Unlike other Cirsium in Korea, Cirsium nipponicum (Island thistle) is distributed only on Ulleung Island, a volcanic island off the east coast of the Korean Peninsula, and a unique thistle with none or very small thorns. Although many researchers have questioned the origin and evolution of C. nipponicum, there is not much genomic information to estimate it. We thus assembled the complete chloroplast of C. nipponicum and reconstructed the phylogenetic relationships within the genus Cirsium. The chloroplast genome was 152,586 bp, encoding 133 genes consisting of 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes. We found 833 polymorphic sites and eight highly variable regions in chloroplast genomes of six Cirsium species by calculating nucleotide diversity, as well as 18 specific variable regions distinguished C. nipponicum from other Cirsium. As a result of phylogenetic analysis, C. nipponicum was closer to C. arvense and C. vulgare than native Cirsium in Korea: C. rhinoceros and C. japonicum. These results indicate that C. nipponicum is likely introduced through the north Eurasian root, not the mainland, and evolved independently in Ulleung Island. This study contributes to further understanding the evolutionary process and the biodiversity conservation of C. nipponicum on Ulleung Island.

The first high-quality genome assembly and annotation of Patiria pectinifera.

The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We assembled the genome using Nanopore and Illumina sequences, yielding a total length of 615 Mb and a scaffold N50 of 24,204,423 bp. Hi-C analysis allowed us to anchor the scaffold sequences onto 22 pseudochromosomes. K-mer based analysis revealed 5.16% heterozygosity rate of the genome, higher than any previously reported echinoderm species. Our transposable element analysis exposed a substantial number of genome-wide retrotransposons and DNA transposons. These results offer valuable resources for understanding the evolutionary mechanisms behind P. pectinifera's successful adaptation in fluctuating environments.

Effects of Thermal Treatment on DC Voltage-Driven Color Conversion in Organic Light-Emitting Diode.

A DC voltage-dependent color-tunable organic light-emitting diode (CTOLED) was proposed for lighting applications. The CTOLED consists of six consecutive organic layers: the hole injection layer, the hole transport layer (HTL), two emission layers (EMLs), a hole blocking layer (HBL), and an electron transport layer (ETL). Only one metal-free phthalocyanine (H2Pc) layer with a thickness of 5 nm was employed as the EML in the CTOLED on a green organic light-emitting diode (OLED) structure using tris (8-hydroxyquinoline) aluminum (III) (Alq3). The current density-voltage-luminance characteristics of the CTOLEDs before and after thermal treatment were characterized and analyzed. Several Gaussian peaks were also extracted by multipeak fitting analysis of the electroluminescent spectra. In the CTOLED before thermal treatment, green emission was dominant in the entire voltage range from low to high voltages, and blue and infrared were emitted simultaneously and at relatively low intensities at low and high voltages, respectively. In the CTOLED after thermal treatment, the dominant color conversion from blue to green was observed as the applied voltage increased, and the infrared emission was relatively low over the entire voltage range. By simulating the CTOLED with and without traps at the H2Pc interface using a technology computer-aided design simulator, we observed the following: 1. After thermal treatment, the CTOLED emitted blue light by exciton generation at the H2Pc-HBL interface because of the small electron transport through the H2Pc thin film due to the dramatic reduction of traps in the low-voltage regime. 2. In the high-voltage regime, electrons reaching the HBL were transferred to Alq3 by resonant tunneling in two quantum wells; thus, green light was emitted by exciton generation at the HTL-Alq3 interface.

Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity.

BACKGROUND: Plazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology. FINDINGS: In total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration. CONCLUSION: This first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.

Thin film encapsulation for quantum dot light-emitting diodes using a-SiN x :H/SiO x N y /hybrid SiO x barriers.

A facile thin film encapsulation (TFE) method having a triple-layered structure of a-SiN x :H/SiO x N y /hybrid SiO x (ASH) on QD-LEDs was performed utilizing both reproducible plasma-enhanced chemical vapor deposition (PECVD) and simple dip-coating processes without adopting atomic layer deposition (ALD). The ASH films fabricated on a polyethylene terephthalate (PET) substrate show a high average transmittance of 88.80% in the spectral range of 400-700 nm and a water vapor transmission rate (WVTR) value of 7.3 × 10-4 g per m2 per day. The measured time to reach 50% of the initial luminance (T50) at initial luminance values of 500, 1000, and 2000 cd m-2 was 711.6, 287.7, and 78.6 h, respectively, and the extrapolated T50 at 100 cd m-2 is estimated to be approximately 9804 h, which is comparable to that of the 12 112 h for glass lid-encapsulated QD-LEDs. This result demonstrates that TFE with the ASH films has the potential to overcome the conventional drawbacks of glass lid encapsulation.

Complete Genome Sequence of Flavobacterium sediminilitoris YSM-43T, Isolated from Tidal Sediment in Yeosu.

Here, we report the complete genome sequence of Flavobacterium sediminilitoris YSM-43T, isolated from a tidal flat in Yeosu, Republic of Korea. The whole genome consists of one circular chromosome of 3,913,692 bp. A total of 3,599 genes were predicted, comprising 3,537 coding DNA sequences (CDSs), 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs).