A5080456763- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Aquaculture disease management and microbiota
- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Reproductive biology and impacts on aquatic species
- Genetic Mapping and Diversity in Plants and Animals
- Marine Bivalve and Aquaculture Studies
- Genetic and phenotypic traits in livestock
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Aquaculture Nutrition and Growth
- Physiological and biochemical adaptations
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Fish Biology and Ecology Studies
- Invertebrate Immune Response Mechanisms
- Lung Cancer Treatments and Mutations
- Animal Genetics and Reproduction
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Fish Ecology and Management Studies
- RNA Research and Splicing
- Cancer, Hypoxia, and Metabolism
- Aquatic Invertebrate Ecology and Behavior
Ocean University of China
2021-2025
Auburn University
2013-2023
University of Chicago
2018-2022
China Medical University
2017
Abstract Catfish represent 12% of teleost or 6.3% all vertebrate species, and are enormous economic value. Here we report a high-quality reference genome sequence channel catfish ( Ictalurus punctatus ), the major aquaculture species in US. The was validated by genetic mapping 54,000 SNPs, annotated with 26,661 predicted protein-coding genes. Through comparative analysis genomes transcriptomes scaled scaleless fish scale regeneration experiments, address genomic basis for most striking...
Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in United States, serves as a great model for analysis against columnaris disease. Channel catfish general highly resistant to disease while blue susceptible. F2 generation hybrids can be produced where phenotypes genotypes are segregating, providing useful system QTL analysis. To identify genes...
Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated recombination often occurring along the length of X Y chromosomes, posing major challenges for identification specific genes. Here, we take an innovative approach comparative genome analysis genomic sequences chromosome newly sequenced channel catfish. Using a YY catfish as sequencing template, generated, assembled, annotated sequence The assembly had...
Increased consumption of omega-3 (ω-3) fatty acids found in cold-water fish and oil has been reported to protect against obesity. A potential mechanism may be through reduction adipocyte differentiation. Stearidonic acid (SDA), a plant-based ω-3 acid, targeted as surrogate for fish-based acids; however, its role differentiation is unknown. This study was designed evaluate the effects SDA on 3T3-L1 cells.3T3-L1 preadipocytes were differentiated presence or vehicle-control. Cell viability...
Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report sequencing and analysis of genome extensive transcriptomes sea cucumber
Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the repetitive fish genomes, we conducted a comparative analysis 52 species 22 orders relation to living aquatic environments. The various genomes were found be positively correlated with genome sizes, few exceptions. More importantly, there appeared specific enrichment between some element categories habitat. Specifically, class II transposons...
Abstract Background The application of RNA-seq has accelerated gene expression profiling and identification gene-associated SNPs in many species. However, the integrated studies along with SNP mapping have been lacking. Coupling bulked segregant analysis (BSA) should allow correlation patterns associated phenotypes. Results In this study, we demonstrated use (BSR-Seq) for differentially expressed genes disease resistance against enteric septicemia catfish (ESC). A total 1,255 were found...
Construction of genetic linkage map is essential for and genomic studies. Recent advances in sequencing genotyping technologies made it possible to generate high-density high-resolution maps, especially the organisms lacking extensive resources. In present work, we constructed a channel catfish with three large resource families genotyped using 250K single-nucleotide polymorphism (SNP) array. A total 54,342 SNPs were placed on map, which our knowledge had highest marker density among...
Abstract Skull morphology is fundamental to evolution and the biological adaptation of species their environments. With aquaculture fish species, head size also important for economic reasons because it has a direct impact on fillet yield. However, little known about underlying genetic basis size. Catfish primary in United States. In this study, we performed genome-wide association study using catfish 250K SNP array with backcross hybrid map QTL (head length, width, depth). One significantly...
The black rockfish (Sebastes schlegelii) is a teleost in which eggs are fertilized internally and retained the maternal reproductive system, where they undergo development until live birth (viviparity). In present study, we report chromosome-level genome assembly. High-throughput transcriptome analysis (RNA-seq ATAC-seq) coupled with situ hybridization (ISH) immunofluorescence reveal several candidate genes for preparation, sperm storage release, hatching. We propose that zona pellucida (ZP)...
Domestication and selection for important performance traits can impact the genome, which is most often reflected by reduced heterozygosity in surrounding genes related to affected selection. In this study, analysis of genomic caused domestication artificial was conducted investigating signatures using single nucleotide polymorphisms (SNPs) channel catfish (Ictalurus punctatus). A total 8.4 million candidate SNPs were identified next generation sequencing. On average, genome harbors one SNP...
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level genome coverage for genomic and genetic analysis because their abundance relatively even distribution in genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed high-density array with 690,662 unique SNPs (herein 690 K array) that were evenly distributed across entire genome, covered 98.6% reference sequence. Here also report...
Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, sometimes "walks" to search for suitable environments during summer. has evolved accessory organs respiring air corresponding mechanisms survive in such challenging environments. Thereby, it serves as great model understanding adaptations terrestrial life.Comparative genomics with channel (Ictalurus punctatus)...
The X and Y chromosomes of channel catfish have the same gene contents. Here, we report allelic hypermethylation chromosome within sex determination region (SDR). Accordingly, X-borne hydin-1 was silenced, whereas Y-borne expressed, making monoallelic expression responsible for determination, much like genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erased epigenetic marks SDR caused reversal genetic females into phenotypic males. After treatment, six other genes...
Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they increasingly degrading due to global climate change local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance conditions that cause bleaching mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. has become a highly invasive species,...
Summary Catfish is the leading aquaculture species in United States. The interspecific hybrid catfish produced by mating female channel with male blue outperform both of their parent a number traits. However, mass production hybrids has been difficult because reproductive isolation. Investigations genome structure and organization provide insights into genetic basis for maintenance divergence face gene flow, thereby helping develop strategies introgression efficient aquaculture. In this...