Project description:Asian salamander Hynobiidae is commonly observed in the Far East Asia regions, including Korea, Japan, China, and the eastern region of Russia. In Korea, there are four Hynobiidae species known to be lived: Hynobius leechii, Hynobius quelpaertensis, Hynobius yangi, and recently reported Hynobius unisacculus. However, even H. leechii which is broadly colonized in Korea peninsula seems to have a new species candidate, which has distinctive genetic and phenotypic characteristics. Genomic resources are essential to understand the current status of these species, but due to the large size of their genomes (about 16 to 20 Gb), it is not easy to analyze. To reveal the genomic characteristics of these species, we constructed more than ten thousands of protein-coding gene sequences from multiple samples of each species, using the de novo transcriptome assembly approach from RNA-Seq data, confirming their taxonomic relationship which was reported based on mitochondrial DNA and marker genes. Also, by comparing previously reported transcriptome of Hynobius chinensis and Hynobius retardatus, lived in China and Japan, respectively, we found that Korean species have unique genetic signatures. By comparing vertebrate model organism genes, we reported Hynobidaii specific proteins. These data would be a useful resource to study other Caudata species in the future. This research was supported by the National Institute of Biological Resources, Republic of Korea, under the project "Genetic diversity of animal resources” (NIBR201703203 and NIBR201803101).
Project description:Root rot disease poses a devastating threat to Coptis chinensis Franch, a medicinal plant prized for its bioactive alkaloids. To dissect its defense mechanisms, we conducted integrated transcriptomic and metabolomic analyses on resistant (R), early-stage infected (S-ES), and late-stage infected (S-LS) plants. Our findings reveal a disease severity-dependent escalation in flavonoid metabolism. Key metabolites, such as kaempferol and quercetin derivatives, were significantly increased compared to R, paralleled by progressive upregulation of biosynthetic genes (PAL, CHS, CHI, FLS). Strikingly, salicylic acid (SA)-associated metabolites and pathway genes (NPR1, NPR3/NPR4) showed no differential expression across groups, contrasting with typical SA-mediated defenses in other species. This study uncovers flavonoid biosynthesis as the primary defense strategy in C. chinensis during root rot progression, while SA signaling may not be the main defense mechanism. These results provide actionable targets for enhancing disease resistance in medicinal plants through metabolic engineering
2025-03-25 | GSE290673 | GEO
Project description:Genome resequencing on Asian icefish Protosalanx chinensis
Project description:Pistacia chinensis Bunge is known as dioecious, but we have found wild monoecious individuals. In order to screen the candidate genes which may influence the sex expression or floral phenotypic differences of P. chinensis, the inflorescence buds for different sex types associated with the sex differentiation were selected and tested for small RNA sequencing. Sex-specific differentially expressed small RNA were discovered, combined with real-time PCR data, the regulation patterns of various sex types were first revealed. Our study represents the first detailed analysis of small RNA sequencing, providing more clues for understanding the mechanism of sex determination on P. chinensis.
Project description:Alternative splicing is pivotal in the genetics of complex traits, but a detailed understanding requires relevant cell types from diverse genetic ancestries. Here, we described cell-type-specific, sex-biased, and ancestry-biased alternative splicing in ~1M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identified widespread sex- and ancestry-biased differentially splicing, most of which are cell-type-specific. We identified 11,577 independent cis-sQTLs, 607 trans-sQTLs, and 107 dynamic sQTLs. Colocalization between cis-eQTL and trans-sQTL revealed a cell-type-specific regulatory relationship between hnRNPLL and PTPRC. We observed a strong enrichment of cis-sQTL effects in autoimmune and inflammatory disease heritability. Specifically, we functionally validated an Asian-specific sQTL disrupting the 5’ splice site of TCHP exon four to putatively modulate the risk of Graves’ disease in East Asian populations. Our work highlights the critical impact of ancestral diversity and provides a roadmap to dissect splicing mechanisms in complex diseases at single-cell resolution.
Project description:Alternative splicing is pivotal in the genetics of complex traits, but a detailed understanding requires relevant cell types from diverse genetic ancestries. Here, we described cell-type-specific, sex-biased, and ancestry-biased alternative splicing in ~1M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identified widespread sex- and ancestry-biased differentially splicing, most of which are cell-type-specific. We identified 11,577 independent cis-sQTLs, 607 trans-sQTLs, and 107 dynamic sQTLs. Colocalization between cis-eQTL and trans-sQTL revealed a cell-type-specific regulatory relationship between hnRNPLL and PTPRC. We observed a strong enrichment of cis-sQTL effects in autoimmune and inflammatory disease heritability. Specifically, we functionally validated an Asian-specific sQTL disrupting the 5’ splice site of TCHP exon four to putatively modulate the risk of Graves’ disease in East Asian populations. Our work highlights the critical impact of ancestral diversity and provides a roadmap to dissect splicing mechanisms in complex diseases at single-cell resolution.
Project description:Transcriptomic profiling of T. chinensis and T. ramosissima shows responses due to water deficit that are common between the two species and differences that shows their invasiveness originating from southern and northern united states. Several drought related genes that were up-regulated common in both species and transcription factors unique to T.chinensis and T. ramosissima were also found. Gene Ontology classification shows similar functional categories in both the species. Differences in two species due to water deficit were also illustrated in networks constructed from genes enriched in biological processes and molecular functions.
Project description:To explore the treatment mechanisms of herbs Pulsatilla chinensis, Bupleurum chinense, and Polyporus umbellatus on lung and liver cancer. We conducted transcriptomic analysis on A549 and Huh7cells treated with these herbs extracts.
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.
