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

Karsi, Attila; Cao, Dongfeng; Li, Ping; Patterson, Andrea; Kocabas, Arif; Feng, Jinian; Zhang, Ju; Mickett, Kathryn; Liu, Zhanjiang

doi:10.1016/s0378-1119(02)00414-6

Cited by 118 publications

(46 citation statements)

References 20 publications

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“…As the ribosome is an indispensable organelle for protein synthesis, high expression of genes encoding ribosomal proteins reinforce their importance in protein translation. Abundant translation activity was reflected in the high transcription levels of the ribosomal protein genes, which was consistent with previous findings (Karsi et al, 2002). Keratin is a fibrous protein that has connective and protective functions, and exists mainly in the epidermal structures of animals.…”

Section: Discussionsupporting

confidence: 91%

Transcriptome expression profiling of fur color formation in domestic rabbits using Solexa sequencing

et al. 2016

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ABSTRACT. Fur color is an important, genetically determined characteristic of domestic rabbits, and rabbit furs are of great economic value. To investigate the molecular genetics associated with fur color determination in domestic rabbits, we used Solexa-sequencing technology to probe gene expression in dorsal skin tissues sampled from full-sibling Rex rabbits of different colors. The number of expressed genes in each sample was approximately 14,700. Among the top 30 genes and transcription factors with the highest reads per kilobase per million values, the elongation factor-alpha 1 gene was highly expressed in all samples, as were genes of the ribosomal protein and keratin gene families. Compared with the chinchilla (C) Rex rabbit control sample, the numbers of genes in the black (B) and white (W) rabbit samples were 1809 and 460, respectively, and the number of common differentially expressed genes was 257. Clustering analysis of these 257 genes revealed that 32 were up-regulated in sample B and down- regulated in sample W. Of these 32 genes, we identified some that are related to fur formation, including Tyrosinase-related protein 1 (TYRP1) and Tyrosinase (TYR), as well as genes with unknown functions. Quantitative real-time polymerase chain reaction was used to verify the expression patterns of those genes. The findings are expected to provide reference for the further study of fur color formation in rabbits.

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Section: Discussionsupporting

confidence: 91%

Transcriptome expression profiling of fur color formation in domestic rabbits using Solexa sequencing

et al. 2016

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“…This limitation significantly affects the application of genomic tools such as microarray technology or real-time quantitative PCR, which provide an integrated overview of the global response at the level of gene expression [334]. While a significant number of genes have been described in immune-related organs, transcriptomic data on peripheral organs barely exist, and the transcriptomic profile of fish skin has been assessed in very few studies [335].…”

Section: Genetic Studies In Fish Skinmentioning

confidence: 99%

An Overview of the Immunological Defenses in Fish Skin

2012

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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.

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“…Compared with tetrapods, only a few studies addressed the molecular structure and developmental expression of S100 genes in teleosts (Ivanenkov et al, 1993;Bobe and Goetz, 2000). In catfish, a homolog of the S100 gene, ictacalcin, had been discovered to be the most abundantly expressed sequence tag (EST) in the chemosensory (Bettini et al, 1994) and skin libraries (Karsi et al, 2002), respectively. By in situ hybridization, Porta and colleagues (1996) demonstrated that ictacalcin gene transcripts are highly detected in epithelial cells of the olfactory rosette, barbel, skin, and gills of adult catfish.…”

Section: Introductionmentioning

confidence: 99%

Skin‐specific expression of ictacalcin, a homolog of the S100 genes, during zebrafish embryogenesis

Hsiao

Ekker

Tsai

2003

Developmental Dynamics

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Full-length cDNA coding for the ictacalcin gene, a homolog of the S100 genes, was isolated in zebrafish and mapped on linkage group 16 using the LN54 radiation hybrid panel. The homology and phylogenetic analyses, based on the deduced amino acid sequences, showed the orthologous relationship of ictacalcin genes between zebrafish and other fish species. However, ictacalcin genes constitute an out-group with respect to other members of the S100 gene family. This result supports the findings that fish ictacalcin genes are new members of the S100 gene family and may have evolved after the divergence of teleosts and tetrapods. The zebrafish ictacalcin gene was zygotically transcribed from 12 hours postfertilization onward and was stably expressed throughout adulthood. During zebrafish embryogenesis, the ictacalcin gene was specifically expressed in striated epidermal cells covering the entire embryo. The ictacalcin staining in keratinocytes of striated epithelia was absent in the cytoplasm surrounding the nuclei, but it was highly concentrated in the peripheral margin. Tissues enriched with epithelia folds, such as olfactory epithelium, hatching gland, pectoral fin buds, urogenital opening, and pharynx, showed a robust ictacalcin expression. The strikingly heavy staining of ictacalcin in the pharyngeal region provides us with an early marker to follow the pharynx formation in zebrafish embryos. Developmental Dynamics 228:745-750, 2003.

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

Cited by 118 publications

References 20 publications

Transcriptome expression profiling of fur color formation in domestic rabbits using Solexa sequencing

Transcriptome expression profiling of fur color formation in domestic rabbits using Solexa sequencing

An Overview of the Immunological Defenses in Fish Skin

Skin‐specific expression of ictacalcin, a homolog of the S100 genes, during zebrafish embryogenesis

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