Genome analysis of Fisheries organisms (KAP220259)
Overall goal: Large-capacity genome / transcriptome / functional gene / genetic marker information produced from 13 species of aquatic organisms can be used as high value-added industrial materials through decoding, analysis, and processing. Completion of standard genome maps for 13 major aquatic organisms (construction of 3 or more types of 3rd generation standard genomes). Development of useful genes and genetic markers related to major economic traits. Establishment of a base for the use of aquatic life-specialized genome database and big data. Discovering high-functional biomaterials derived from aquatic organism genome big data  2nd year goal: Investigation of useful gene functions of 4 aquatic organisms and production of new aquatic organism genome information . Useful gene discovery and functional study of Gadus chalcogrammus, Platichthys stellatus,  Amphiprion clarkii, and Periophthalmus magnuspinnatus. . Genome and transcriptome analysis of Misgurnus mizolepis, Thamnaconus modestus, Epinephelus akaara, Scomber japonicus, Anguilla japonica, Silurus asotus, etc. . Fish microbiome analysis . Analysis and processing of large-capacity omics information. Genome and transcript analysis of target species for genome decoding in the 2nd year (Misgurnus mizolepis, Thamnaconus modestus, Epinephelus akaara, Scomber japonicus, Anguilla japonica, Silurus asotus, etc.). 2nd year genome decoding method and scope: Based on the genome size of 1.0 Gb. Production of homozygous transcripts for annotation: Full-length expression gene analysis using IsoSeq: Brain, gills, liver, kidney, spleen, stomach, pylorus, intestine, muscle, shell, blood cell, gonad RNA after pooling in equal amounts. Comparative analysis of genomes of related species: [Misgurnus mizolepis] Comparative genomes of Misgurraus anguillicaudatus and Paramisg; urnus dabryanus, a similar species. Microbiome analysis: [Hypomesus nipponensis] 16S rRNA sequencing and colony analysis of surface and intestinal microbes, comparative analysis of beneficial bacteria and pathogenic bacteria genomes, functional analysis of fish consumption using mice, blood indicators, analysis of changes in intestinal microbes, and health functional analysis. Gene function analysis: comparative analysis of expression patterns by tissue and condition of water temperature or immune-related genes, and functional analysis through recombinant protein or peptide synthesis. Discovery of biomarkers and biomaterials based on genome information: Simple sequence repeat extraction based on genome and transcriptome sequences, MS marker development for species and population analysis, and candidates based on physicochemical conditions (pI, net charge, secondary structure, etc.) specific to antibacterial peptides Investigation of antibacterial activity through peptide synthesis after mass extraction of peptide sequences. Establishment of chromosome-level standard genome: [Scomber japonicus] Chromosome-level data production of International Vertebral Animal Genome Project (VGP)'. Develop useful genes and genetic markers related to major economic traits (disease, growth, etc.). Identification of useful gene functions. Establishment of aquatic life-specialized data platform. Discovering functional biomaterials based on genome big data  1) Technical aspects. World leader in comparative genomics: Leading the field of comparative genomics through the development of innovative comparative genomic analysis tools that are not only tailored to the new third-generation standard genome format, but also provide new research opportunities for structural variation analysis, which was previously limited. expect.. Securing the 3rd Generation Standard Genome Construction Pipeline: The first attempt to construct the 3rd generation standard genome at the chromosome level, which is not yet present in Korea, establishes and secures the pipeline, providing a foundation for future research.. Laying the foundation for subsequent multiomics research: Establishing a high-quality standard genome will provide domestic and foreign researchers a foothold for integrated research from a multiomics perspective such as transcriptomics, metabolomics, and epigenomics.  2) Economic and industrial aspects. Diversification of farmed fish species and molecular breeding: It is expected that it will be used for breeding in the future by breaking away from the current fishing practice that is focused on some fish species and securing genetic markers and genomic information for more diverse species.. Discovery and utilization of new genetic resources for marine organisms: Useful genetic resources such as antibacterial peptides are discovered from various marine organisms, and specific application plans are sought.. Prepare for profit sharing of genetic resources: In accordance with the Nagoya Protocol's benefit-sharing agreement on Digital Sequence Information (DSI), the standard genome information produced in this project will be used as an advantageous factor for Korea in the global competition for genetic resources.  3) Social aspect. Transmission of genetic resources for future generations: By constructing genome information of endemic and endangered species in the form of standard genomes at the chromosome level, high-quality genetic information about the relevant species is recorded and delivered to future generations.. Basic research for biodiversity conservation: Based on the understanding of the specific genetic characteristics of each species, the evolutionary adaptation mechanism and ecological adaptation can be understood more deeply and can be used for future biodiversity conservation based on this.