Earticle

Cinnamomum camphora (Lauraceae) is an evergreen broad-leaved tree and distributed in the south of China and Japan. This species has been widely cultivated in many countries because of its aromatic oils, insect-repellent effects and ornamental value. Despite its vast utilization and cultivation, little is known about its genetic diversity and population genetics. To date, only a few genomic simple sequence repeat (SSR) markers were developed in C. camphora and no genic-SSR primers were available yet. Thus, it is necessary to develop more genic-SSR markers, which will facilitate the genetic studies of Cinanamomum. In this study, a total of 74,289 simple sequence repeats (SSRs) were found in 56,124 unigenes, of which 14,225 unigenes contained more than one SSR locus. Among these SSR loci, the mono-nucleotide repeats were the most frequent, with a frequency of 61.14%, followed by 24.87% di-nucleotide repeats and 12.87% tri-nucleotide repeats. Twenty-one polymorphic SSR markers were developed and validated in 45 camphor trees. The 21 loci were further examined for genetic diversity of 38 provenances, 190 individuals in the whole natural distribution area of camphor tree in China. The results showed that 74 polymorphic sites were detected with average 2.74 polymorphic were detected for each prime. The means of observed and expected heterozygosities were 0.4446 and 0.4419, respectively. Nei's and Shannon’s information index for these populations were 0.4400 and 0.7193, respectively. The genetic similarity coefficient of 38 provenances was between 0.05 and 0.95, with an average of 0.17.The smallest genetic distance is JXWY and JXRJ and the genetic distance between JXTG and GZDZ was the largest. Cluster analysis in 0.88 genetic distance can divide into five groups. Jiangxi provenances clustered into two groups, of which JXAY grouped into one group and other provenances grouped into another group. Other provenances of China grouped three small branches: CQYY and HNHH, GZDZ and SCLZ, and other provenances. The clustering results showed that the genetic components of camphor tree in China had obvious regional features. The analysis of molecular variance exhibited that 77% of genetic variation was observed within the populations. The novel genic-SSR markers will not only benefit genetic diversity analysis and wild resources conservation of C. camphora, but also contribute to exploring the further evolutionary history and genetic differentiation pattern of Cinnamomum.

Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and Haemophilus parasuis (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV?HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV?HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) were consistent with those determined by high-throughput sequencing. In the PRRSV?HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, competitive endogenous RNA (ceRNA) networks of different groups were constructed, and the ssc-miR-671-5p miRNA was validated as a potential regulatory factor to regulate DTX4 and AEBP1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.

Wheat gluten is an increasingly common ingredient in poultry diets but its impact on the small intestine in chicken is not fully understood. This study aimed to identify effects of high-gluten diets on chicken small intestines and the variation of their associated transcriptional responses by age. A total of 120 broilers (Ross Strain) were used to perform two animal experiments consisting of two gluten inclusion levels (0% or 25%) by bird’s age (1 week or 4 weeks). Transcriptomics and histochemical techniques were employed to study the effect of gluten on their duodenal mucosa using randomly selected 12 broilers (3 chicks per group). A reduction in feed intake and body weight gain was found in the broilers fed a high-gluten containing diet at both ages. Histochemical photomicrographs showed a reduced villus height to crypt depth ratio in the duodenum of gluten-fed broilers at 1 week. We found mainly a significant effect on the gene expression of duodenal mucosa in gluten-fed broilers at 1 week (289 differentially expressed genes [DEGs]). Pathway analyses revealed that the significant DEGs were mainly involved in ribosome, oxidative phosphorylation, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. These pathways are involved in ribosome protein biogenesis, oxidative phosphorylation and fatty acid metabolism, respectively. Our results suggest a pattern of differential gene expression in these pathways that can be linked to chronic inflammation, suppression of cell proliferation, cell cycle arrest and apoptosis. And via such a mode of action, high-gluten inclusion levels in poultry diets could lead to the observed retardation of villi development in the duodenal mucosa of young broiler chicken.

Nutritional studies in the cattle typically focus on the rumen and its microbial environment, leaving other parts of the gastrointestinal (GI) tract largely unexplored. Thus, underlying molecular mechanisms and the responses to dietary treatment in the lower gut is poorly understood. In this study, we investigated the caecum transcriptome changes and its associated microbial communities in calves with or without artificially dosed rumen content extracted from an adult cow. Eight calves were included in the study, four received artificially dosed adult rumen content (Treated) and the rest received autoclaved rumen content as a control. We observed significant transcriptome changes in the caecum between treatments, with 1,836 differentially expressed genes (DEGs) identified. A predominant portion of the DEGs were down-regulated in the treated group, which showed significant enrichment for molecular pathways related to immune response, host response to pathogens, and inflammatory responses. For the DEGs correlated with the highest number of microbes, gene ontology analysis indicated an enrichment in pathways associated with inflammation and immune response. By comparing the microbial taxa abundance among different GI tissues collected from the same study, we observed that the same dosing strategy may lead to differential retention of the microbial community in different GI tract locations. Our work indicated that the hind gut showed robust response to artificial dosing and the caecum microbial community may interact extensively with the host to shape the development and maturity of the host immune system in early life. Furthermore, our analysis suggested that tissue-specific analysis is required to fully understand the impact of early dosing on animal performance and physiology.

Background: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance. Results: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type (p ≤ 0.05). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized. Conclusions: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong(Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST searchagainst the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotatedand classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as wellas in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembranetransporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgorpressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantlydetected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefoliusaccession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuableresource for understanding the structure and function of the ginseng transcriptomes.

After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.

Protein-translated mRNA analysis has been extensively used to determine the function of various traits in animals. The non-coding RNA (ncRNA), which was known to be non-functional because it was not encoded as a protein, was re-examined as it was studied to actually function. One of the ncRNAs, long non-coding RNA (lncRNA), is known to have a function of regulating mRNA expression, and its importance is emerging. Therefore, lncRNAs are currently being used to understand the traits of various animals as well as human diseases. However, studies on lncRNA annotation and its functions are still lacking in most animals except humans and mice. lncRNAs have unique characteristics of lncRNAs and interact with mRNA through various mechanisms. In order to make lncRNA annotations in animals in the future, it is essential to understand the characteristics of lncRNAs and the mechanisms by which lncRNAs function. In addition, this will allow lncRNAs to be used for a wider variety of traits in a wider range of animals, and it is expected that integrated analysis using other biological information will be possible.

Background: In the aftermath of September 11 attacks, the radiobiology community sought novel radiation mitigators capable of preventing death when administered 24 hours or later after exposure to lethal ionizing radiation. The survival and expansion of normal stem cells are crucial for restoring tissue integrity in time to prevent mortality. While U.S. Food and Drug Administration- approved drugs for acute radiation syndrome primarily target the hematopoietic system, restoring the integrity of the intestinal lining is equally important for survival. However, the radiation response of the intestinal stem cell (ISC) population and its niche environment is not as well understood as that of the bone marrow. The aim of this study is to explore early transcriptomic changes in the small intestine after a lethal dose of total body irradiation (TBI) and during subsequent recovery. Materials and Methods: C3H/Sed/Kam mice were irradiated with a TBI dose of 16 Gy, the published 70% lethal dose within 10 days. The compound 1-[(4-nitrophenyl)sulfonyl]-4-phenylpiperazine (NSPP) was administered 24 hours post-irradiation. RNAs from the proximal duodenum were extracted at 28, 72, and 96 hours post-irradiation and subjected to RNA-sequencing. Differentially expressed genes were analyzed using gene-set enrichment analysis. Results and Discussion: Radiation induced significant transcriptomic changes known to precede the death of lymphatic endothelial and epithelial cells. Upregulation of Lgr5+ ISC gene signature was observed during recovery. NSPP treatment further amplified the activation of ISCassociated genes and other regenerative markers. Notably, gene Psrc1 showed strong activation throughout the recovery process, highlighting its potential role in this regenerative response. Conclusion: Our findings highlight potential additional intervention points for mitigating radiation- induced damage in the intestines beyond solely targeting programmed cell death. These insights may contribute to the development of more effective radioprotective approaches, ultimately improving clinical outcomes for individuals undergoing radiotherapy or exposed to highdose radiation.

The range of possible growth temperature of the Lentinula edodes mycelium is 5~32℃, and the appropriate temperature is 22~26℃, which is generally known as medium and high temperature. In order to check the expression level of the gene according to the temperature during growth, the temperature was divided into three treatments of 10, 20, and 30℃ to grow the altitude, and 20℃ was used as a control. The result is as follows. a total of 32,706 genes were identified, and 1319 genes were identified at 10℃ compared to the control for those with a more than 2-fold change expression level. among them, 591 genes were up-regulated at 10℃ compared to the control. it was confirmed that 728 genes were down-regulated, and those grown at 30°C were 6,977 genes that expressed more than 2 fold change compared to the control, and the number of up-regulated genes was 3,703 down-regulated. 3,274 genes were identified. among the upregulated genes, cytochrome P450, Alpha beta hydrolase fold protein, chondroitin AC alginate lyase, and proline-specific peptidase were identified. Among the downregulated genes, farnesyl-diphosphate synthase, zinc finger transcription factor 1, and glycolytic enzyme family 79 proteins were identified.

In this study, we extracted RNA of Pleurotus ostreatus fruiting body treated 10, 100ppm Mepiquat chloride dry weight of sawdust medium. Result of fruiting body’s mRNA-seq, 12460 genes are fold changed and contrast 2-fold-change 149 genes including tRNA-His, tRNA-Thr, tRNA-pro, carbohydrate esterase family 16 protein, etc. are up-regulated and 64 genes including QCR9, subunit of the ubiquinol cytochrome-c reductase complex, glycoside hydrolase family 17 protein, carbohydrate-binding module family 13 protein etc. are down-regulated at 10, 100ppm

The color of the Pleurotus ostreatus pileus is black, gray to yellow, and pink to yellow, etc. the transcriptomes of the white Pleurotus ostreatus "Baekseon" and the black Pleurotus ostreatus "Heuktari" with different shades were analyzed to confirm the difference between the color of the Pleurotus ostreatus and the amount of gene expression. The results are as follows. As a result of the analysis of oyster transcripts, 12,460 genes were expressed, and 1080 genes were identified with an expression level of 2-fold change or more. Among them, 536 genes were up-regulated and 544 were down-regulated. Among the up-regulated genes, carbohydrate esterase family 1 protein, glycosyltransferase family 58 protein, cora superfamily, and copper-amine-oxidase superfamily were identified. Among the down-regulated genes, polysaccharide lyase family 3 protein, cytochrome C1 protein, pleurotolysin B precursor Etc. were confirmed.

The ascomycete fungus Cordyceps militaris infects lepidopteran insect pupae, forming characteristic fruiting bodies called “Dong Chung Ha Cho” in Korean. They have been used as medicines owing to their anti-allergic, anti-inflammatory, and immune-enhancing effects. This fungus can be grown on the geminated soybeans Rhynchosia nulubilis, which also contains several novel isoflavones. We performed a comparative transcriptome analysis to determine core gene sets or pathways contributing to biologically active products such as isoflavone. Initially, we sequenced 2-week-old fungal cultures on different soybean agar media, where different amounts of water agar were implemented to show different surface topology. We selected 830 upregulated and 188 downregulated genes by comparing linear models of the samples (two-fold change threshold). Gene ontology analysis identified that the “IMP biosynthesis” term was significantly found in the upregulated gene sets. The pathway is involved in the synthesis of cordycepin, the reference chemical for C. militaris. This finding in the transcriptome data is consistent with the previous observation: increased cordycepin concentrations in the C. militaris cultured on germinated soybean.

Streptomyces produce various secondary metabolites including antibiotics which are used in medical and agricultural fields. The production of these compounds occurs after passing through the transition from primary metabolism to secondary metabolism. Despite the significant attributions of Streptomyces to biotechnological area, their gene regulation and antibiotics production mechanisms are not fully discovered. Here we show gene expression patterns in different developmental phases to analyze the genes involved in antibiotics production using strand specific RNA-seq method. The analyzed result indicates experimental proof for operon structures and transcription units in Streptomyces and shows novel transcripts including small RNAs, thus allowing better understanding of the genome architecture of Streptomyces coelicolor. [This work was supported by Intelligent Synthetic Biology Center (2011-0031957, 2011-0031962)]

Mannheimia succiniciproducens, a gram-negative rumen bacterium producing succinic acid, was adapted to medium with high-concentration of succinic acid for acid tolerance. Responses of the adapted M. succiniciproducens strain to succinic acid shock were investigated based on transcriptome analysis. During the investigations, gene expression levels of the adapted M. succiniciproducens strain were compared with a parent strain and the expression patterns after acid shock are classified refer to function of genes. Standing on the transcriptome data, specific genes of M. succiniciproducens are selected as targets of genetic manipulations. To improve tolerance for succinic acid, It was tried that overexpression or knock-out experiments of target genes and finding global regulators for acid resistance. [This work was supported by the Genome-Based Integrated Bioprocess Development Project from the Korean Ministry of Education, Science and Technology (No. 2005-01304). Further supports by LG Chem Chair Professorship, and WCU (World Class University) program through the National Research Foundation of Korea are greatly appreciated.]

Genome-scale metabolic network modeling and simulation have played important roles in metabolic engineering. Its key role is to integrate omics data with metabolic network for more accurate prediction. We hypothesized that there might exist genes showing changes in their expression correlated with their corresponding flux values upon perturbations. These flux-coupled genes (FCGs) were investigated using transcriptome and 13C-fluxdataof Escherichia coli, and most consistent FCGs were identified as gnd, pfkB, rpe, sdhB, sdhD, sucA, and zwf. The corresponding reactions were then given additional constraints in flux balance analysis (FBA). This results were also compared with conventional simulation methods. This strategy is expected to be useful due to the relative easiness of obtaining a few genes’ transcriptional information. [This work was supported by the Technology Development Program to Solve Climate Changes (systems metabolic engineering for biorefineries) from the Ministry of Education, Science and Technology (MEST) through the National Research Foundation of Korea (NRF-2012-C1AAA001-2012M1A2A2026556)]