The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken).

BACKGROUND: Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS: The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS: Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.

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 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 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.

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.

Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations.

Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value [Formula: see text] and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise [Formula: see text] in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles.

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.

The idiosyncratic genome of Korean long-tailed chicken as a valuable genetic resource.

Today, breeds with ornamental traits such as exceptionally long tail feathers are economically valuable. However, the genetic basis of long-tail feathers is yet to be understood. To provide better understanding of long tail feathers, we sequenced Korean long-tailed chicken (KLC) genomes and compared them with genomes of other chicken breeds. We first analyzed the genome structure of KLC and its genomic relationship with other chickens and observed unique characteristics. Subsequently, we searched for genomic regions under selection. Feather keratin 1-like enriched region and several genes were found to have novel putative functions and effects on the long tail trait in KLC. Our findings support the value of KLC as a unique genetic resource and cast light on the genetic basis of long tail traits in avian species. We expect this novel knowledge to provide new genomic evidence and options for designing and implementing genetic improvements of ornamental chicken productivity through precision crossbreeding aids.

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.

Crystal Structure and Regiospecificity of Catechol O-Methyltransferase from Niastella koreensis.

Catechol O-methyltransferase (COMT) is an enzyme that transfers a methyl group to the catechol-derivative substrates using S-adenosyl-l-methionine (SAM) and Mg2+. We report the biochemical and structural analysis of COMT from Niastella koreensis (NkCOMT). NkCOMT showed the highest activity with Mg2+, although the enzyme also showed a significant level of activity with Cu2+ and Zn2+. NkCOMT structures complexed with SAH and Mg2+ elucidated how the enzyme stabilized the cosubstrate and the metal ion and revealed that the region near the SAM binding site undergoes conformational changes upon the binding of the cosubstrate and the metal ion. We also identified the catechol binding pocket of the enzyme and explained a broad substrate specificity of the bacterial enzyme and its ability to accommodate the catechol derivatives. In addition, we developed the NkCOMTE211R and NkCOMTE211K variants that showed both enhanced activities and regiospecificity for the production of the para-forms. Our study provides a structural basis for regiospecificity of NkCOMT, which is related with the conformational change upon binding of SAM and Mg2+.

Structural and Functional Characterization of Cystathionine γ-lyase from Bacillus cereus ATCC 14579.

Cysteine is a semiessential amino acid and plays an important role in metabolism and protein structure and has also been applied in various industrial fields, such as pharmaceutical, food, cosmetic, and animal feed industries. Metabolic engineering studies have been conducted for the cysteine production through bacterial fermentation, but studies on the cysteine biosynthetic pathway in microorganisms are limited. We report the biochemical characteristics of cystathionine γ-lyase from Bacillus cereus ATCC 14579 (BcCGL). We also determined the crystal structure of BcCGL in complex with the PLP cofactor and identified the substrate binding mode. We observed that the replacement of the conserved Glu321 residue to alanine showed increased activity by providing wider active site entrance and hydrophobic interaction for the substrate. We suggest that the structural differences of the α13-α14 region in CGL enzymes might determine the active site conformation.

Effects of Allium hookeri on gut microbiome related to growth performance in young broiler chickens.

Healthy food promotes beneficial bacteria in the gut microbiome. A few prebiotics act as food supplements to increase fermentation by beneficial bacteria, which enhance the host immune system and health. Allium hookeri is a healthy food with antioxidant and anti-inflammatory activities. A. hookeri is used as a feed supplement for broiler chickens to improve growth performance. Although the underlying mechanism is unknown, A. hookeri may alter the gut microbiome. In the current study, 16S rRNA sequencing has been carried out using samples obtained from the cecum of broiler chickens exposed to diets comprising different tissue types (leaf and root) and varying amounts (0.3% and 0.5%) of A. hookeri to investigate their impact on gut microbiome. The microbiome composition in the groups supplemented with A. hookeri leaf varied from that of the control group. Especially, exposure to 0.5% amounts of leaf resulted in differences in the abundance of genera compared with diets comprising 0.3% leaf. Exposure to a diet containing 0.5% A. hookeri leaf decreased the abundance of the following bacteria: Eubacterium nodatum, Marvinbryantia, Oscillospira, and Gelria. The modulation of gut microbiome by leaf supplement correlated with growth traits including body weight, bone strength, and infectious bursal disease antibody. The results demonstrate that A. hookeri may improve the health benefits of broiler chickens by altering the gut microbiome.

Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome.

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.