Attila Karsi

Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin.

Previous molecular genetic studies on channel catfish (Ictalurus punctatus) have focused on limited number of genes and gene products. Recent advancement of molecular techniques made high throughput analysis of transcriptomes possible. As part of our transcriptome analysis of channel catfish, we have analyzed 1909 expressed sequence tags (ESTs) derived from a skin library. Of the 1909 ESTs analyzed, 1376 (72.1%) ESTs representing 496 unique genes had homologies with other organisms while 478 (25.0%) ESTs had no significant homologies and were designated as unknown. The remaining 55 (2.9%) EST clones were eliminated because of their low quality or short sequences. Of the 496 unique genes, 327 (65.9%) genes were singletons while 169 (34.1%) genes represented by two or more ESTs. A total of 1007 (52.8%) ESTs representing 235 unique genes matched previously reported channel catfish ESTs while 847 (44.4%) ESTs representing 261 unique genes were newly identified from this research. Functional categorization of the channel catfish genes indicated that the largest group was ribosomal proteins with 65 unique genes represented by 500 clones. The most abundantly expressed gene, the calcium binding protein ictacalcin, accounted for almost 5% of overall expression, indicating its important function in the skin. Sequence analysis of ESTs revealed the presence of 89 microsatellite-containing genes that may be valuable for future mapping studies.

Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain

Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the brain mRNA of channel catfish (Ictalurus punctatus). As part of our transcriptome analysis in catfish to develop molecular reagents for comparative functional genomics, here we report analysis of 1201 brain cDNA clones. Of the 1201 clones, 595 clones (49.5%) were identified as known genes by BLAST searches and 606 clones (50.5%) as unknown genes. The 595 clones of known gene products represent transcripts of 251 genes. These known genes were categorized into 15 groups according to their biological functions. The largest group of known genes was the genes involved in translational machinery (21.4%) followed by mitochondrial genes (6.2%), structural genes (3.1%), genes homologous to sequences of unknown functions (2.3%), enzymes (2.7%), hormone and regulatory proteins (2.5%), genes involved in immune systems (2.1%), genes involved in sorting, transport, and metal metabolism (1.8%), transcriptional factors and DNA repair proteins (1.6%), proto-oncogenes (1.2%), lipid binding proteins (1.2%), stress-induced genes (0.7%), genes homologous to human genes involved in mental diseases (0.6%), and development or differentiation-related genes (0.3%). The number of genes represented by the 606 clones of unknown genes is not known at present, but the high percentage of clones showing no homology to any known genes in the GenBank databases may indicate that a great number of novel genes exist in teleost brain.

Expression Profile of the Channel Catfish Spleen : Analysis of Genes Involved in Immune Functions

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.

Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli

Despite recent advances in sequencing, complete finishing of large genomes and analysis of novel proteins they encode typically require cloning of specific regions. However, many of these fragments are extremely difficult to clone in current vectors. Superhelical stress in circular plasmids can generate secondary structures that are substrates for deletion, particularly in regions that contain numerous tandem or inverted repeats. Common vectors also induce transcription and translation of inserted fragments, which can select against recombinant clones containing open reading frames or repetitive DNA. Conversely, transcription from cloned promoters can interfere with plasmid stability. We have therefore developed a novel Escherichia coli cloning vector (termed ‘pJAZZ’ vector) that is maintained as a linear plasmid. Further, it contains transcriptional terminators on both sides of the cloning site to minimize transcriptional interference between vector and insert. We show that this vector stably maintains a variety of inserts that were unclonable in conventional plasmids. These targets include short nucleotide repeats, such as those of the expanded Fragile X locus, and large AT—rich inserts, such as 20-kb segments of genomic DNA from Pneumocystis, Plasmodium, Oxytricha or Tetrahymena. The pJAZZ vector shows decreased size bias in cloning, allowing more uniform representation of larger fragments in libraries.

Development of Polymorphic EST Markers Suitable for Genetic Linkage Mapping of Catfish

Abstract: Expressed sequence tag (EST) markers are important for gene mapping and for marker-assisted selection (MAS). To develop EST markers for use in catfish gene mapping, 100 randomly picked complementary DNAs from the channel catfish (Ictalurus punctatus) pituitary library were sequenced. The EST sequences were used to design primers to amplify channel catfish and blue catfish (I. furcatus) genomic DNAs. Polymerase chain reaction products of the ESTs were analyzed to determine length polymorphism between the channel catfish and blue catfish. Eleven polymorphic EST markers were identified. Five of the 11 EST markers were from known genes and the other six were from unidentified ESTs. Seven ESTs were found to be associated with microsatellite sequences. Analysis of channel catfish gene sequences indicated highly biased codon usage, with 16 codons being preferably used. These codons were more preferably used in highly expressed ribosomal protein genes and in highly expressed pituitary hormone genes. G/C-rich codons are less used in channel catfish than those in other vertebrates suggesting AT-richness of the channel catfish genome.

Effects of Insert Size on Transposition Efficiency of the Sleeping Beauty Transposon in Mouse Cells

Abstract: Transposon vectors are widely used in prokaryotic and lower eukaryotic systems. However, they were not available for use in vertebrate animals until the recent reconstitution of a synthetic fish transposon, Sleeping Beauty (SB). The reacquisition of transposability of the SB transposase fostered great enthusiasm for using transposon vectors as tools in vertebrate animals, particularly for gene transfer to facilitate accelerated integration of transgenes into chromosomes. Here, we report the effects of insert sizes on transposition efficiency of SB. A significant effect of insert size on efficiency of transposition by SB was found. The SB transposase enhanced the integration efficiency effectively for SB transposon up to approximately 5.6 kb, but lost its ability to enhance the integration efficiency when the transposon size was increased to 9.1 kb. This result indicates that the SB transposon system is highly applicable for transferring small genes, but may not be applicable for transferring very large genes.

Genetic and virulence characterization of Flavobacterium columnare from channel catfish (Ictalurus punctatus)

Aim:  To develop a method for conducting pulsed‐field gel electrophoresis (PFGE) on Flavobacterium columnare, to use PFGE to characterize F. columnare channel catfish isolates, and to determine whether variation in pathogenic potential exists in F. columnare isolates from channel catfish.

Translational machinery of channel catfish : I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression

Ribosomal protein (RP) genes have become widely used as markers for phylogenetic studies and comparative genomics. However, they have not been available for evolutionary studies in fish although teleosts are the largest group of vertebrates with more than 23,000 species. Using a transcriptomic approach, we have cloned and sequenced 32 40S RP complementary DNAs (cDNAs) from channel catfish (Ictalurus punctatus), making them one of the most complete sets of 40S RP gene sequences from a single organism. Most 40S RPs in channel catfish are highly similar to their orthologues in mammalian species, but S19, S21, and S25 are highly divergent. Only one type of cDNA was found for all RP genes except S26 and S27, for which two cDNAs were found in channel catfish. Alternatively spliced transcripts for the S3 and alternatively polyadenylated transcripts for S19 and S21 were found. The 32 40S RP genes are generally highly expressed and together they account for 5.33-11.42% of expression depending on the tissues. Expression levels of the RP genes were highly variable both within a single tissue among different RP genes and among tissues with regard to a single RP gene. Taken together, these data strongly suggest post-transcriptional regulation of RP gene expression, particularly in consideration of the stoichiometry of their representation in ribosomes.

Genome Sequence of the Fish Pathogen Flavobacterium columnare ATCC 49512

Flavobacterium columnare is a Gram-negative, rod-shaped, motile, and highly prevalent fish pathogen causing columnaris disease in freshwater fish worldwide. Here, we present the complete genome sequence of F. columnare strain ATCC 49512.

Channel Catfish Follicle-Stimulating Hormone and Luteinizing Hormone: Complementary DNA Cloning and Expression During Ovulation

Abstract: Gonadotropins are important regulators of reproduction. To develop molecular resources for production of recombinant gonadotropins, we have cloned and sequenced complementary DNA encoding the channel catfish (Ictalurus punctatus) follicle-stimulating hormone (FSH) and luteinizing hormone (LH), which encode 132 and 140 amino acid proteins, respectively. The deduced amino acid sequences of the catfish FSH and LH are highly conserved with those cloned from other teleosts. Both the FSH and the LH were highly induced during ovulation after injection of carp pituitary extract. Taken together with our previous findings of enhanced expression of growth hormone and other pituitary hormones, this research suggests that a hormonal cocktail may be needed for more efficient manipulation of catfish reproduction. The availability of the catfish FSH and LH cDNAs provides the opportunity for production of immunologically or biologically active recombinant gonadotropins for the study of catfish reproductive physiology and the manipulation of artificial spawning for aquaculture.