Full length article Transcriptome immunomodulation of in-feed additives in Atlantic salmon Salmo salar infested with sea lice Caligus rogercresseyi Gustavo Nú ~ nez-Acu ~ na a , Ana Teresa Gonçalves a , Valentina Valenzuela-Mu ~ noz a , Jorge Pino-Marambio b , Simon Wadsworth c , Cristian Gallardo-Esc  arate a, * a Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, University of Concepci on, Concepci on, Chile b Ewos Innovation Chile, Camino a Pargua km 57, Colaco km 5, Calbuco, Chile c Ewos Innovation Norway, N-4335 Dirdal, Norway article info Article history: Received 20 May 2015 Received in revised form 31 August 2015 Accepted 2 September 2015 Available online 10 September 2015 Keywords: RNA-seq In-feed additives Head kidney Skin Caligus rogercresseyi Salmo salar abstract One of the most significant threats to the Chilean salmon aquaculture industry is the ectoparasitic sea louse Caligus rogercresseyi. To cope with sea lice infestations, functional diets have become an important component in strengthening the host immune response. The aim of this study was to evaluate molecular mechanisms activated through immunostimulation by in-feed plant-derived additives in Atlantic salmon infected with sea lice. Herein, a transcriptome-wide sequencing analysis was performed from skin and head kidney tissues, evidencing that the immune response genes were the most variable after the challenge, especially in the head kidney, while other genes involved in metabolism were highly expressed individuals fed with the immunostimulants. Interestingly, defensive enzymes such as Cyto- chrome p450 and serpins were down-regulated in infested individuals, especially in skin tissue. Addi- tionally, MHC-I and MHC-II genes were differentially expressed after the incorporation of the in-feed additives, giving some cues about the protection mechanisms of plant-derived compound as immu- nostimulants for infested salmons. This is the first published study that evaluates the transcriptomic response of sea lice-infested Atlantic salmon fed with in-feed additives. © 2015 Elsevier Ltd. All rights reserved. 1. Introduction For the last decade, Chile has been a leading worldwide aqua- culture producer, second only to Norway. However, this industry depends in large part on Atlantic salmon (Salmo salar) farming, which reached its peak in 2008 [1]. Despite considerable produc- tion efforts, this industry has been significantly impacted by sani- tary issues, resulting in a multidimensional crisis [2]. Currently there is serious concern about the presence of parasites, particu- larly sea lice, and the sanitary and economic consequences of these in salmon farming [3]. Caligidosis is the sea lice parasitosis affecting the Chilean in- dustry. Caused by Caligus rogercresseyi, this ectoparasite has caused high economic losses in recent years [4]. Most of these costs are due to the treatments used to control this disease, which generally consist in chemical compounds that attack the parasite's biological processes, such as molting and nervous system functions [5]. Additionally, these antiparasitic drugs have diverse environmental impacts on non-target species and marine habitats [6e10], and some are highly persistent in the marine environment [11]. Considering the above, there is an urgent need to develop novel control strategies for sea lice infestations in salmon farms. A diversity of defense responses to marine ectoparasitic co- pepods have been studied over the last decades in various fish species, including physiological, cellular, and molecular responses [12]. The Atlantic salmon has evidenced varied physiological re- sponses to Northern hemisphere sea lice (Lepeophtheirus salmonis) infestations, such as increases in mucus production, cell mucus proliferation, tissue erosion, and inflammation of the affected tis- sues [13e16]. These responses are modulated depending on fish welfare and the lifecycle stage of the parasite. Short-term sea lice exposure assays produced stress responses in S. salar , increasing cortisol levels and the transcription of genes involved in coping * Corresponding author. Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Con- cepci on, Barrio Universitario s/n, Centro de Biotecnología, P.O. Box 160-C, Con- cepci on, Chile. E-mail addresses: crisgallardo@udec.cl, crisgallardo@oceanografia.udec.cl (C. Gallardo-Esc arate). Contents lists available at ScienceDirect Fish & Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi http://dx.doi.org/10.1016/j.fsi.2015.09.009 1050-4648/© 2015 Elsevier Ltd. All rights reserved. Fish & Shellfish Immunology 47 (2015) 450e460