Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

Abstract

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally >10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

An Overview of the Immunological Defenses in Fish Skin

“…These studies will enable future gene expression analysis of skin. The relevance of skin as a defensive organ against pathogens and parasites is increased through the identification of several immune relevant genes, both of the innate and adaptive system [362]. In this transcriptome several isotigs exhibiting homology to mammalian mucins (MUC2, MUC5AC and MUC5B) have been identified [362].…”

Aeromonas salmonicida Binds Differentially to Mucins Isolated from Skin and Intestinal Regions of Atlantic Salmon in an N -Acetylneuraminic Acid-Dependent Manner

“…Five orthologues of these have been identified in the genome of the pufferfish, Fugu rubripes (26), and 13 orthologues have been identified in the genome of the zebrafish, Danio rerio (27). Next-generation sequencing of salmon skin has revealed partial mucin sequences with homology to the human MUC2 and MUC5 mucins (28). However, knowledge on the composition and function of the fish mucins in pathogen defense is scarce.…”

Aditivos Mucogénicos para el Control de Caligus rogercresseyi en Salmón del Atlántico (Salmo salar)

“…Son pocos los genes de mucina (MUC) que se han identificado en teleósteos que codifican para estas proteínas (Micallef et al, 2012). En la carpa, dos genes de mucina se han caracterizado: MUC2 y MUC5B, exhibiendo homología con las mucinas de mamí-feros (Marel et al, 2012).…”

“…El conocimiento de la composición y la función de las mucinas en los peces para la defensa contra los patógenos es escaso (Padra et al, 2014). Además, el transcriptoma de la piel del salmón del Atlántico está mal caracterizado (Micallef et al, 2012). En el estudio de Guardiola et al (2014), para determinar los componentes del mucus de los peces, se observaron resultados de unión a lectina, indicando que el moco de la piel contiene en orden de abundancia, ácido, glucosa, N-acetil-glucosamina, galactosa, fructosa y residuos de N-acetilneuramínico; asimismo, se observó que algunas actividades inmunes fueron muy similares en los peces estudiados (actividad de la lisozima, por ejemplo, IgM), pero que otras, tales como proteasa, antiproteasa, fosfatasa alcalina, esterasas y peroxidasa variaban dependiendo de las especies.…”