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Author

Yu Zhang

Bio: Yu Zhang is an academic researcher from Ocean University of China. The author has contributed to research in topics: Catfish & Genome. The author has an hindex of 18, co-authored 33 publications receiving 1400 citations. Previous affiliations of Yu Zhang include Auburn University & Chinese Academy of Fishery Sciences.

Papers
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Journal ArticleDOI
TL;DR: A high-quality reference genome sequence of channel catfish is reported, providing evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish and demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.
Abstract: Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance. Catfish represent 6.3% of all vertebrate species, and occupy a phylogenetic position close to the common ancestor of bony fish. Liu et al. present a reference genome of the channel catfish, and reveal a genomic basis for the evolutionary loss of scales in these species.

237 citations

Journal ArticleDOI
TL;DR: The results set a foundation for future studies comparing mechanisms of pathogen entry and mucosal immunity across several important catfish pathogens including E. ictaluri, Edwardsiellatarda, Flavobacterium columnare, and virulent atypical Aeromonas hydrophila.

195 citations

Journal ArticleDOI
TL;DR: This is the first RNA-Seq-based expression study in catfish in response to heat stress, and the candidate genes identified should be valuable for further targeted studies on heat tolerance, thereby assisting the development of heat-tolerant catfish lines for aquaculture.
Abstract: Temperature is one of the most prominent abiotic factors affecting ectotherms. Most fish species, as ectotherms, have extraordinary ability to deal with a wide range of temperature changes. While the molecular mechanism underlying temperature adaptation has long been of interest, it is still largely unexplored with fish. Understanding of the fundamental mechanisms conferring tolerance to temperature fluctuations is a topic of increasing interest as temperature may continue to rise as a result of global climate change. Catfish have a wide natural habitat and possess great plasticity in dealing with environmental variations in temperature. However, no studies have been conducted at the transcriptomic level to determine heat stress-induced gene expression. In the present study, we conducted an RNA-Seq analysis to identify heat stress-induced genes in catfish at the transcriptome level. Expression analysis identified a total of 2,260 differentially expressed genes with a cutoff of twofold change. qRT-PCR validation suggested the high reliability of the RNA-Seq results. Gene ontology, enrichment, and pathway analyses were conducted to gain insight into physiological and gene pathways. Specifically, genes involved in oxygen transport, protein folding and degradation, and metabolic process were highly induced, while general protein synthesis was dramatically repressed in response to the lethal temperature stress. This is the first RNA-Seq-based expression study in catfish in response to heat stress. The candidate genes identified should be valuable for further targeted studies on heat tolerance, thereby assisting the development of heat-tolerant catfish lines for aquaculture.

134 citations

Journal ArticleDOI
TL;DR: The large set of transcripts assembled in this study is the most comprehensive set of genome resources ever developed from catfish, which will provide the much needed resources for functional genome research inCatfish, serving as a reference transcriptome for genome annotation, analysis of gene duplication, gene family structures, and digital gene expression analysis.
Abstract: Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriously hindered by genome duplication. Because of gene duplications, one cannot establish orthologies simply by homology comparisons. Rather intense phylogenetic analysis or structural analysis of orthologies is required for the identification of genes. To conduct phylogenetic analysis and orthology analysis, full-length transcripts are essential. Generation of large numbers of full-length transcripts using traditional transcript sequencing is very difficult and extremely costly. In this work, we took advantage of a doubled haploid catfish, which has two sets of identical chromosomes and in theory there should be no allelic variations. As such, transcript sequences generated from next-generation sequencing can be favorably assembled into full-length transcripts. Deep sequencing of the doubled haploid channel catfish transcriptome was performed using Illumina HiSeq 2000 platform, yielding over 300 million high-quality trimmed reads totaling 27 Gbp. Assembly of these reads generated 370,798 non-redundant transcript-derived contigs. Functional annotation of the assembly allowed identification of 25,144 unique protein-encoding genes. A total of 2,659 unique genes were identified as putative duplicated genes in the catfish genome because the assembly of the corresponding transcripts harbored PSVs or MSVs (in the form of pseudo-SNPs in the assembly). Of the 25,144 contigs with unique protein hits, around 20,000 contigs matched 50% length of reference proteins, and over 14,000 transcripts were identified as full-length with complete open reading frames. The characterization of consensus sequences surrounding start codon and the stop codon confirmed the correct assembly of the full-length transcripts. The large set of transcripts assembled in this study is the most comprehensive set of genome resources ever developed from catfish, which will provide the much needed resources for functional genome research in catfish, serving as a reference transcriptome for genome annotation, analysis of gene duplication, gene family structures, and digital gene expression analysis. The putative set of duplicated genes provide a starting point for genome scale analysis of gene duplication in the catfish genome, and should be a valuable resource for comparative genome analysis, genome evolution, and genome function studies.

123 citations

Journal ArticleDOI
TL;DR: Four QTLs associated with columnaris resistance in catfish are revealed and many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host.
Abstract: 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 the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). A genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host. The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance.

112 citations


Cited by
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01 Jan 2001
TL;DR: Genetical genomics as discussed by the authors combines the power of genomics and genetics in a way that is likely to become instrumental in the further unravelling of metabolic, regulatory and developmental pathways.
Abstract: The recent successes of genome-wide expression profiling in biology tend to overlook the power of genetics. We here propose a merger of genomics and genetics into ‘genetical genomics’. This involves expression profiling and marker-based fingerprinting of each individual of a segregating population, and exploits all the statistical tools used in the analysis of quantitative trait loci. Genetical genomics will combine the power of two different worlds in a way that is likely to become instrumental in the further unravelling of metabolic, regulatory and developmental pathways.

952 citations

Journal ArticleDOI
TL;DR: The current knowledge of the immunological defences present in skin mucosa is summarised as a very important part of the fish immune system, serving as an anatomical and physiological barrier against external hazards.
Abstract: The vertebrate immune system is comprised of numerous distinct and interdependent components Every component has its own inherent protective value, and the final combination of them is likely to be related to an animal’s immunological history and evolutionary development Vertebrate immune system consists of both systemic and mucosal immune compartments, but it is the mucosal immune system which protects the body from the first encounter of pathogens According to anatomical location, the mucosa-associated lymphoid tissue, in teleost fish is subdivided into gut-, skin-, and gill-associated lymphoid tissue and most available studies focus on gut The purpose of this paper is to summarise the current knowledge of the immunological defences present in skin mucosa as a very important part of the fish immune system, serving as an anatomical and physiological barrier against external hazards Interest in defence mechanism of fish arises from a need to develop health management tools to support a growing finfish aquaculture industry, while at the same time addressing questions concerning origins and evolution of immunity in vertebrates Increased knowledge of fish mucosal immune system will facilitate the development of novel vaccination strategies in fish

532 citations

01 Jan 2000
TL;DR: A type III protein secretion system encoded by Salmonella pathogenicity island 2 (SPI2) has been found to be required for virulence and survival within macrophages as discussed by the authors.
Abstract: A type III protein secretion system encoded by Salmonella pathogenicity island 2 (SPI2) has been found to be required for virulence and survival within macrophages. Here, SPI2 was shown to allow Salmonella typhimurium to avoid NADPH oxidase-dependent killing by macrophages. The ability of SPI2-mutant bacteria to survive in macrophages and to cause lethal infection in mice was restored by abrogation of the NADPH oxidase-dependent respiratory burst. Ultrastructural and immunofluorescence microscopy demonstrated efficient localization of the NADPH oxidase in the proximity of vacuoles containing SPI2-mutant but not wild-type bacteria, suggesting that SPI2 interferes with trafficking of oxidase-containing vesicles to the phagosome.

531 citations

Journal Article
TL;DR: Fish embryos provide excellent animal models for understanding the regulatory roles of IGF, IGF receptor and IGF-binding proteins in vertebrate embryonic development, and current research on the developmental and nutritional role of IGF in fish will undoubtedly contribute to knowledge of the basic physiology of vertebrates in general.
Abstract: The insulin-like growth factors (IGF) are evolutionarily ancient growth factors present in all vertebrates. The central importance of IGF for normal development and growth has been illustrated by the severe growth-retarded phenotype exhibited by IGF-I, IGF-II or IGF-I receptor knockout mice. Although we know much about the gross effects of IGF on the overall size of the fetus and the clinical manifestations that result from fetal and neonatal deficiency of IGF (i.e., severe growth retardation leads to dwarfism), very little is known about the in vivo actions of IGF during embryogenesis at the cellular and molecular levels. Most research on the developmental role of IGF has relied on rodent models, and attempts to elucidate the molecular and cellular basis of IGF actions have been hampered by the inaccessibility of the mammalian fetus enclosed in the uterus. During the past decade, there has been growing support for the concept that the IGF have been highly conserved in all vertebrates. Both IGF-I and IGF-II are present in fish, and their structures are highly conserved. Human and fish IGF-I are equally potent in mammalian and fish bioassay systems. Insulin-like growth factor mRNA is found in all life stages of fish, ranging from unfertilized egg to adult. The temporal and spatial expression pattems of fish IGF-I seem to be similar to those in mammals. Nutritional status and growth hormone both have a profound effect on IGF-I expression in fish, as they do in mammals. These features suggest that the IGF system is highly conserved between teleost fish and mammals. Because fish embryos develop extemally, they provide excellent animal models for understanding the regulatory roles of IGF, IGF receptor and IGF-binding proteins in vertebrate embryonic development. Current research on the developmental and nutritional roles of IGF in fish will undoubtedly contribute to knowledge of the basic physiology of vertebrates in general.

357 citations