Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture sp... more Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation because of its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in male channel catfish normally starts between 90 and 102 days postfertilization (dpf), while the ovarian differentiation starts early from 19 dpf. As such, efforts to better understand the postponed testicular development at the molecular level are needed. Toward that end, we conducted transcriptomic comparison of gene expression of male and female gonads at 90, 100, and 110 dpf using high-throughput RNA-Seq. Transcriptomic profiles of male gonads on 90 and 100 dpf exhibited high similarities except for a small number of significantly up-regulated genes that were involved in development of germ cell-supporting somatic cells, while drastic changes were observed during 100-110 dpf, with a group of highly up-regulated genes that were involved in germ cells development, including nanog and pou5f1. Transcriptomic comparison between testes and ovaries identified male-preferential genes, such as gsdf, cxcl12, as well as other cytokines mediated the development of the gonad into a testis. Coexpression analysis revealed highly correlated genes and potential pathways underlying germ cell differentiation and spermatogonia stem cell development. The candidate genes and pathways identified in this study set the foundation for further studies on sex determination and differentiation in catfish as well as other teleosts.
Background Channel catfish and blue catfish are the most important aquacultured species in the US... more Background Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. Results We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as...
Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an id... more Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an identical gene content of 950 genes each. In this study, we conducted comparative analyses of methylome and transcriptome of genetic males and genetic females before gonadal differentiation to provide insights into the mechanisms of sex determination. Differentially methylated CpG sites (DMCs) were predominantly identified on the sex chromosome, most notably within the sex determination region (SDR), although the overall methylation profiles across the entire genome were similar between genetic males and females. The drastic differences in methylation were located within the SDR at nucleotide position 14.0–20.3 Mb of the sex chromosome, making this region an epigenetically marked locus within the sex determination region. Most of the differentially methylated CpG sites were hypermethylated in females and hypomethylated in males, suggesting potential involvement of methylation modification ...
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major impor... more Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.
The current study was conducted to assess the effects of microinjection of different dosages of g... more The current study was conducted to assess the effects of microinjection of different dosages of guide RNA (gRNA)/Cas9 protein on the mutation rate, embryo survival, embryonic development, hatchability and early fry survival in channel catfish, Ictalurus punctatus. Guide RNAs targeting two of the channel catfish immune-related genes, toll/interleukin 1 receptor domain-containing adapter molecule (TICAM 1) and rhamnose binding lectin (RBL) genes, were designed and prepared. Three dosages of gRNA/Cas9 protein (low, 2.5 ng gRNA/7.5 ng Cas9, medium, 5 ng gRNA/15 ng Cas9 and high, 7.5 ng gRNA/22.5 ng Cas9) were microinjected into the yolk of one-cell embryos. Mutation rate increased with higher dosages (p < 0.05). Higher dosages increased the mutation frequency in individual embryos where biallelic mutations were detected. For both genes, microinjection procedures increased the embryo mortality (p < 0.05). Increasing the dosage of gRNA/Cas9 protein increased the embryo mortality and...
Molecular genetics and genomics : MGG, Jan 12, 2017
Growth is the most important economic trait in aquaculture. Improvements in growth-related traits... more Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was f...
Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathoge... more Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathogenassociated molecular patterns and use conserved signaling pathways to activate proinflammatory cytokines and type-1 interferons to fight infection. TLR3 in mammals is best known for its recognition of dsRNA as ligand and its MyD88-independent signaling. TLR3, upon recognition of dsRNA, recruits and binds its adaptor protein TIR domaincontaining adapter molecule (TICAM) 1. Here we report the genomic sequences and structures of TLR3 and a TICAM adaptor from channel catfish (Ictalurus punctatus). Whereas a partial TLR3 cDNA sequence has been reported from channel catfish, and complete TLR3 genes are known from other teleost fish species, a complete TICAM sequence has not been previously reported from a nonmammalian species. Analysis of catfish TLR3 and TICAM expression after infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggested a conserved TLR3-TICAM receptor-adaptor relation in catfish. Comparison of TLR3 and TICAM expression profiles in channel catfish with those from the closely related blue catfish species (Ictalurus furcatus), which exhibits strong resistance to ESC, revealed a striking pattern of species-specific expression. A dramatic downregulation of TLR3 and TICAM gene expression was observed in blue catfish head kidney and spleen, which we speculate may be the result of maturation and migration of different cell types to and from the lymphoid tissues following infection.
Background: Sex determination mechanisms in teleost fish broadly differ from mammals and birds, w... more Background: Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach of comparative genome analysis of the genomic sequences of the X chromosome and newly sequenced Y chromosome in the channel catfish. Results: Using a YY channel catfish as the sequencing template, we generated, assembled, and annotated the Y genome sequence of channel catfish. The genome sequence assembly had a contig N50 size of 2.7 Mb and a scaffold N50 size of 26.7 Mb. Genetic linkage and GWAS analyses placed the sex determination locus within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Instead, comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of the breast cancer anti-resistance 1 (BCAR1) gene in the male during early sex differentiation. Experimental knockout of BCAR1 gene converted genetic males (XY) to phenotypic females, suggesting BCAR1 as a putative sex determination gene. Conclusions: We present the first Y chromosome sequence among teleost fish, and one of the few whole Y chromosome sequences among vertebrate species. Comparative analyses suggest that sex-specific isoform expression through alternative splicing may underlie sex determination processes in the channel catfish, and we identify BCAR1 as a potential sex determination gene.
Regulatory regions of the (3-actin gene of the common carp (Cyprinus carpio) have been examined b... more Regulatory regions of the (3-actin gene of the common carp (Cyprinus carpio) have been examined by linking upstream, 5'-flanking sequences and regions of the first intron to a bacterial chloramphenicol acetyltransferase (CAT) reporter gene. By analysis of the mRNA products and encoded CAT activity, we have identified four
Transgenic fish have been developed that have improved growth, color, disease resistance, sur- vi... more Transgenic fish have been developed that have improved growth, color, disease resistance, sur- vival in cold, and body composition, and produce pharmaceutical proteins. Transgenes elicit pleiotropic effects, some positive and some negative. In general, transgenic fish appear to have lower fitness than controls and pose little environmental risk, but this research is not fully con- clusive. Transgenic zebrafish with altered coloration have been commercialized and growth hor- mone transgenic salmon, carp, and tilapia are near commercialization. To enhance commer- cialization and minimize environmental risk, additional technologies such as transgenic steriliza- tion need to be developed. Genomic research has produced an abundance of molecular genet- ic information including many genes for consideration for gene transfer, highly regulated gene promoters, and knowledge about their expression and function. Functional genomics analysis should be applied in the future to enhance the capacit...
Repetitive elements make up significant proportions of genomes. However, their roles in evolution... more Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched a...
Comparative biochemistry and physiology. Part D, Genomics & proteomics, Mar 23, 2016
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particul... more Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome. A total of eight taste receptor genes were identified, including five type I and three type II taste receptor genes. Their genomic locations, phylogenetic relations, orthologies and expression were determined. Phylogenetic and collinear analyses provided understanding of the evolution dynamics of this gene family. Furthermore, the motif and dN/dS analyses indicated that selection pressures of different degrees were imposed on these receptors. Additionally, four genes of gus...
Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey... more Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey within a certain distance. This can be compensated through detecting specific water-soluble substances by the olfactory receptors (ORs) and trace amine associated receptors (TAARs) expressed on the olfactory epithelium. We identified the OR and TAAR repertoires in channel catfish, and characterized the genomic organizations of these two gene families by data mining available genomic resources. A total of 47 putative OR genes and 36 putative TAAR genes were identified in the channel catfish genome, including 27 functional OR genes and 28 functional TAAR genes. Phylogenetic and orthogroup analyses were conducted to illustrate the evolutionary dynamics of the vertebrate ORs and TAARs. Collinear analysis revealed the presence of two conserved orthologous blocks that contain OR genes between the catfish genome and the zebrafish genome. The complete loss of a conserved motif in fish OR family...
*Department of Genetics and Cell Biology, University of Minnesota, St Paul, MN 55108, USA tPerman... more *Department of Genetics and Cell Biology, University of Minnesota, St Paul, MN 55108, USA tPermanent address: Institute of Hydrobiology, Academia Sinica, Wuhan, Hubei, People's Republic of China +Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, ...
Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origi... more Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 different...
Molecular genetics and genomics : MGG, Jan 8, 2016
Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE).... more Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE). In this work, we analyzed ASE in F1 hybrid catfish using RNA-Seq datasets. While the vast majority of genes were expressed with both alleles, 7-8 % SNPs exhibited significant differences in allele ratios of expression. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5420 (8.2 %) and 13,390 (7.5 %) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 1519 and 3075 ASE-genes were identified. Gene Ontology analysis revealed that genes encoding cytoplasmic ribosomal proteins (RP) were highly enriched among ASE genes. Parent-of-origin was determined for 27 and 30 ASE RP genes in the liver and gill, respectively. The results indicated that genes from both channel catfish and blue catfish were involved in ASE. However, each RP gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in...
... Doctoral dissertation Auburn, Alabama: Auburn University. 3. Bart, AN and Dunham, RA 1996. ..... more ... Doctoral dissertation Auburn, Alabama: Auburn University. 3. Bart, AN and Dunham, RA 1996. ... Transactions of the American Fisheries Society, 125: 580–586. [CrossRef]; 15. Walser, CA andPhelps, RP 1993. Factors influencing the enumeration of channel catfish eggs. ...
A family of highly repetitive DNA sequences referred to as Xba elements was identified and charac... more A family of highly repetitive DNA sequences referred to as Xba elements was identified and characterized from the channel catfish (Ictalurus punctatus) genome. The Xba elements represent about 5% to 6% of the total genomic DNA of the channel catfish. The Xba elements are distributed specifically in the channel catfish and blue catfish (I. furcatus), but not in closely related species such as white catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris). These Xba elements are arranged as head-to-tail tandem repeats. Seven sequences were sequenced. They are A/T-rich (over 65%). Each sequence contains four copies of the ATTA repeat and eight copies of (A)3-6 GT/TG motifs whose function is not known. Each unit of the repeats is 325 bp from the Kansas strain, and 321 pb from the Auburn and Stuttgart strains of channel catfish. The Xba elements are conserved in length within a specific strain, and highly conserved in sequence identity. Sequence identity is more conserved amon...
Both qualitative and quantitative patterns of tissue-specific gene expression can be determined u... more Both qualitative and quantitative patterns of tissue-specific gene expression can be determined using gene profiling. Expressed sequence tag (EST) analysis is an efficient approach not only for gene discovery and examining gene expression, but also for development of molecular resources useful for functional genomics. As part of an ongoing transcriptome analysis of channel catfish (Ictalurus punctatus), EST analysis was conducted for gene annotations and profiling using a complementary DNA library developed from messenger RNA of the spleen. A total of 1204 spleen cDNA clones were analyzed. Of the 1204 clones, 665 clones (55.2%) were identified as orthologs of known genes from other organisms by BLAST searches and 539 clones (44.8%) as unknown gene clones. In total 147 novel genes were identified, and annotations were made to 118 of them. In addition, 389 novel EST clusters were identified. Expression profile was analyzed in relation to metabolic functional groups. A total of 28 known genes were involved in immune functions, of which 10 were identified for the first time in channel catfish. Microsatellite-containing clones were also identified that may be potentially useful for genome mapping. This work contributed to the Catfish Gene Index, and toward a Unigene set useful for functional genomics research concerning spleen gene functions in relation to disease defenses.
Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture sp... more Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation because of its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in male channel catfish normally starts between 90 and 102 days postfertilization (dpf), while the ovarian differentiation starts early from 19 dpf. As such, efforts to better understand the postponed testicular development at the molecular level are needed. Toward that end, we conducted transcriptomic comparison of gene expression of male and female gonads at 90, 100, and 110 dpf using high-throughput RNA-Seq. Transcriptomic profiles of male gonads on 90 and 100 dpf exhibited high similarities except for a small number of significantly up-regulated genes that were involved in development of germ cell-supporting somatic cells, while drastic changes were observed during 100-110 dpf, with a group of highly up-regulated genes that were involved in germ cells development, including nanog and pou5f1. Transcriptomic comparison between testes and ovaries identified male-preferential genes, such as gsdf, cxcl12, as well as other cytokines mediated the development of the gonad into a testis. Coexpression analysis revealed highly correlated genes and potential pathways underlying germ cell differentiation and spermatogonia stem cell development. The candidate genes and pathways identified in this study set the foundation for further studies on sex determination and differentiation in catfish as well as other teleosts.
Background Channel catfish and blue catfish are the most important aquacultured species in the US... more Background Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. Results We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as...
Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an id... more Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an identical gene content of 950 genes each. In this study, we conducted comparative analyses of methylome and transcriptome of genetic males and genetic females before gonadal differentiation to provide insights into the mechanisms of sex determination. Differentially methylated CpG sites (DMCs) were predominantly identified on the sex chromosome, most notably within the sex determination region (SDR), although the overall methylation profiles across the entire genome were similar between genetic males and females. The drastic differences in methylation were located within the SDR at nucleotide position 14.0–20.3 Mb of the sex chromosome, making this region an epigenetically marked locus within the sex determination region. Most of the differentially methylated CpG sites were hypermethylated in females and hypomethylated in males, suggesting potential involvement of methylation modification ...
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major impor... more Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.
The current study was conducted to assess the effects of microinjection of different dosages of g... more The current study was conducted to assess the effects of microinjection of different dosages of guide RNA (gRNA)/Cas9 protein on the mutation rate, embryo survival, embryonic development, hatchability and early fry survival in channel catfish, Ictalurus punctatus. Guide RNAs targeting two of the channel catfish immune-related genes, toll/interleukin 1 receptor domain-containing adapter molecule (TICAM 1) and rhamnose binding lectin (RBL) genes, were designed and prepared. Three dosages of gRNA/Cas9 protein (low, 2.5 ng gRNA/7.5 ng Cas9, medium, 5 ng gRNA/15 ng Cas9 and high, 7.5 ng gRNA/22.5 ng Cas9) were microinjected into the yolk of one-cell embryos. Mutation rate increased with higher dosages (p < 0.05). Higher dosages increased the mutation frequency in individual embryos where biallelic mutations were detected. For both genes, microinjection procedures increased the embryo mortality (p < 0.05). Increasing the dosage of gRNA/Cas9 protein increased the embryo mortality and...
Molecular genetics and genomics : MGG, Jan 12, 2017
Growth is the most important economic trait in aquaculture. Improvements in growth-related traits... more Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was f...
Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathoge... more Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathogenassociated molecular patterns and use conserved signaling pathways to activate proinflammatory cytokines and type-1 interferons to fight infection. TLR3 in mammals is best known for its recognition of dsRNA as ligand and its MyD88-independent signaling. TLR3, upon recognition of dsRNA, recruits and binds its adaptor protein TIR domaincontaining adapter molecule (TICAM) 1. Here we report the genomic sequences and structures of TLR3 and a TICAM adaptor from channel catfish (Ictalurus punctatus). Whereas a partial TLR3 cDNA sequence has been reported from channel catfish, and complete TLR3 genes are known from other teleost fish species, a complete TICAM sequence has not been previously reported from a nonmammalian species. Analysis of catfish TLR3 and TICAM expression after infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggested a conserved TLR3-TICAM receptor-adaptor relation in catfish. Comparison of TLR3 and TICAM expression profiles in channel catfish with those from the closely related blue catfish species (Ictalurus furcatus), which exhibits strong resistance to ESC, revealed a striking pattern of species-specific expression. A dramatic downregulation of TLR3 and TICAM gene expression was observed in blue catfish head kidney and spleen, which we speculate may be the result of maturation and migration of different cell types to and from the lymphoid tissues following infection.
Background: Sex determination mechanisms in teleost fish broadly differ from mammals and birds, w... more Background: Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach of comparative genome analysis of the genomic sequences of the X chromosome and newly sequenced Y chromosome in the channel catfish. Results: Using a YY channel catfish as the sequencing template, we generated, assembled, and annotated the Y genome sequence of channel catfish. The genome sequence assembly had a contig N50 size of 2.7 Mb and a scaffold N50 size of 26.7 Mb. Genetic linkage and GWAS analyses placed the sex determination locus within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Instead, comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of the breast cancer anti-resistance 1 (BCAR1) gene in the male during early sex differentiation. Experimental knockout of BCAR1 gene converted genetic males (XY) to phenotypic females, suggesting BCAR1 as a putative sex determination gene. Conclusions: We present the first Y chromosome sequence among teleost fish, and one of the few whole Y chromosome sequences among vertebrate species. Comparative analyses suggest that sex-specific isoform expression through alternative splicing may underlie sex determination processes in the channel catfish, and we identify BCAR1 as a potential sex determination gene.
Regulatory regions of the (3-actin gene of the common carp (Cyprinus carpio) have been examined b... more Regulatory regions of the (3-actin gene of the common carp (Cyprinus carpio) have been examined by linking upstream, 5'-flanking sequences and regions of the first intron to a bacterial chloramphenicol acetyltransferase (CAT) reporter gene. By analysis of the mRNA products and encoded CAT activity, we have identified four
Transgenic fish have been developed that have improved growth, color, disease resistance, sur- vi... more Transgenic fish have been developed that have improved growth, color, disease resistance, sur- vival in cold, and body composition, and produce pharmaceutical proteins. Transgenes elicit pleiotropic effects, some positive and some negative. In general, transgenic fish appear to have lower fitness than controls and pose little environmental risk, but this research is not fully con- clusive. Transgenic zebrafish with altered coloration have been commercialized and growth hor- mone transgenic salmon, carp, and tilapia are near commercialization. To enhance commer- cialization and minimize environmental risk, additional technologies such as transgenic steriliza- tion need to be developed. Genomic research has produced an abundance of molecular genet- ic information including many genes for consideration for gene transfer, highly regulated gene promoters, and knowledge about their expression and function. Functional genomics analysis should be applied in the future to enhance the capacit...
Repetitive elements make up significant proportions of genomes. However, their roles in evolution... more Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched a...
Comparative biochemistry and physiology. Part D, Genomics & proteomics, Mar 23, 2016
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particul... more Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome. A total of eight taste receptor genes were identified, including five type I and three type II taste receptor genes. Their genomic locations, phylogenetic relations, orthologies and expression were determined. Phylogenetic and collinear analyses provided understanding of the evolution dynamics of this gene family. Furthermore, the motif and dN/dS analyses indicated that selection pressures of different degrees were imposed on these receptors. Additionally, four genes of gus...
Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey... more Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey within a certain distance. This can be compensated through detecting specific water-soluble substances by the olfactory receptors (ORs) and trace amine associated receptors (TAARs) expressed on the olfactory epithelium. We identified the OR and TAAR repertoires in channel catfish, and characterized the genomic organizations of these two gene families by data mining available genomic resources. A total of 47 putative OR genes and 36 putative TAAR genes were identified in the channel catfish genome, including 27 functional OR genes and 28 functional TAAR genes. Phylogenetic and orthogroup analyses were conducted to illustrate the evolutionary dynamics of the vertebrate ORs and TAARs. Collinear analysis revealed the presence of two conserved orthologous blocks that contain OR genes between the catfish genome and the zebrafish genome. The complete loss of a conserved motif in fish OR family...
*Department of Genetics and Cell Biology, University of Minnesota, St Paul, MN 55108, USA tPerman... more *Department of Genetics and Cell Biology, University of Minnesota, St Paul, MN 55108, USA tPermanent address: Institute of Hydrobiology, Academia Sinica, Wuhan, Hubei, People's Republic of China +Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, ...
Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origi... more Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 different...
Molecular genetics and genomics : MGG, Jan 8, 2016
Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE).... more Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE). In this work, we analyzed ASE in F1 hybrid catfish using RNA-Seq datasets. While the vast majority of genes were expressed with both alleles, 7-8 % SNPs exhibited significant differences in allele ratios of expression. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5420 (8.2 %) and 13,390 (7.5 %) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 1519 and 3075 ASE-genes were identified. Gene Ontology analysis revealed that genes encoding cytoplasmic ribosomal proteins (RP) were highly enriched among ASE genes. Parent-of-origin was determined for 27 and 30 ASE RP genes in the liver and gill, respectively. The results indicated that genes from both channel catfish and blue catfish were involved in ASE. However, each RP gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in...
... Doctoral dissertation Auburn, Alabama: Auburn University. 3. Bart, AN and Dunham, RA 1996. ..... more ... Doctoral dissertation Auburn, Alabama: Auburn University. 3. Bart, AN and Dunham, RA 1996. ... Transactions of the American Fisheries Society, 125: 580–586. [CrossRef]; 15. Walser, CA andPhelps, RP 1993. Factors influencing the enumeration of channel catfish eggs. ...
A family of highly repetitive DNA sequences referred to as Xba elements was identified and charac... more A family of highly repetitive DNA sequences referred to as Xba elements was identified and characterized from the channel catfish (Ictalurus punctatus) genome. The Xba elements represent about 5% to 6% of the total genomic DNA of the channel catfish. The Xba elements are distributed specifically in the channel catfish and blue catfish (I. furcatus), but not in closely related species such as white catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris). These Xba elements are arranged as head-to-tail tandem repeats. Seven sequences were sequenced. They are A/T-rich (over 65%). Each sequence contains four copies of the ATTA repeat and eight copies of (A)3-6 GT/TG motifs whose function is not known. Each unit of the repeats is 325 bp from the Kansas strain, and 321 pb from the Auburn and Stuttgart strains of channel catfish. The Xba elements are conserved in length within a specific strain, and highly conserved in sequence identity. Sequence identity is more conserved amon...
Both qualitative and quantitative patterns of tissue-specific gene expression can be determined u... more Both qualitative and quantitative patterns of tissue-specific gene expression can be determined using gene profiling. Expressed sequence tag (EST) analysis is an efficient approach not only for gene discovery and examining gene expression, but also for development of molecular resources useful for functional genomics. As part of an ongoing transcriptome analysis of channel catfish (Ictalurus punctatus), EST analysis was conducted for gene annotations and profiling using a complementary DNA library developed from messenger RNA of the spleen. A total of 1204 spleen cDNA clones were analyzed. Of the 1204 clones, 665 clones (55.2%) were identified as orthologs of known genes from other organisms by BLAST searches and 539 clones (44.8%) as unknown gene clones. In total 147 novel genes were identified, and annotations were made to 118 of them. In addition, 389 novel EST clusters were identified. Expression profile was analyzed in relation to metabolic functional groups. A total of 28 known genes were involved in immune functions, of which 10 were identified for the first time in channel catfish. Microsatellite-containing clones were also identified that may be potentially useful for genome mapping. This work contributed to the Catfish Gene Index, and toward a Unigene set useful for functional genomics research concerning spleen gene functions in relation to disease defenses.
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Papers by Zhanjiang Liu