Abstract
Fish skin serves as the first line of defense against a wide variety of chemical, physical and biological stressors. Secretion of mucus is among the most prominent characteristics of fish skin and numerous innate immune factors have been identified in the epidermal mucus. However, molecular mechanisms underlying the mucus secretion and immune activities of fish skin remain largely unclear due to the lack of genomic and transcriptomic data for most economically important fish species. In this study, we characterized the skin transcriptome of mud loach using Illumia paired-end sequencing. A total of 40364 unigenes were assembled from 86.6 million (3.07 gigabases) filtered reads. The mean length, N50 size and maximum length of assembled transcripts were 387, 611 and 8670 bp, respectively. A total of 17336 (43.76%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. Gene ontology mapping assigned a total of 108513 GO terms to 15369 (38.08%) unigenes. KEGG orthology mapping annotated 9337 (23.23%) unigenes. Among the identified KO categories, immune system is the largest category that contains various components of multiple immune pathways such as chemokine signaling, leukocyte transendothelial migration and T cell receptor signaling, suggesting the complexity of immune mechanisms in fish skin. As for mucin biosynthesis, 37 unigenes were mapped to 7 enzymes of the mucin type O-glycan biosynthesis pathway and 8 members of the polypeptide N-acetylgalactosaminyltransferase family were identified. Additionally, 38 unigenes were mapped to 23 factors of the SNARE interactions in vesicular transport pathway, indicating that the activity of this pathway is required for the processes of epidermal mucus storage and release. Moreover, 1754 simple sequence repeats (SSRs) were detected in 1564 unigenes and dinucleotide repeats represented the most abundant type. These findings have laid the foundation for further understanding the secretary processes and immune functions of loach skin mucus.
Highlights
Fish skin has vital biological functions including chemical and physical protection, sensory activity, behavioral purposes, thermoregulation, hormone metabolism, maintenance of fluid balance and osmotic homeostasis [1,2]
Due to the lack of genomic and transcriptomic data for non-model fish species, identification and characterization of bioactive substances produced by fish epidermis have been conducted using conventional biochemical methods, which restricts the ability of researchers to uncover the full repertoire of mucous substances
Multiple k-mer values can be used by Oases and SOAPdenovoTrans, while the version of Trinity used in this study takes a single k-mer value of 25
Summary
Fish skin has vital biological functions including chemical and physical protection, sensory activity, behavioral purposes, thermoregulation, hormone metabolism, maintenance of fluid balance and osmotic homeostasis [1,2]. As the interface between environment and the inner body, fish skin is persistently exposed to environmental stressors and provides an important first line of defense against the attachment and penetration of various invading pathogens [5,6,7]. The epidermal mucus is suggested to be one of the most important protective substances associated with fish skin [8]. This notion is supported by the isolation and identification of numerous immune factors in fish skin mucus, including immunoglobulins, antimicrobial peptides, lysozymes, protease, lectins, C-reactive protein and complement proteins [9,10,11,12,13,14,15,16,17,18,19,20]. Molecular mechanisms underlying the development and maturation of mucous cells, the synthesis and release of mucus bioactive products, and the responses of mucus cells to environmental stressors and pathogens remain largely unknown
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