Contents lists available at ScienceDirect Fish and Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi Full length article Transcriptome analysis identifies immune-related genes and antimicrobial peptides in Siamese fighting fish (Betta splendens) Piti Amparyup a,b,* , Walaiporn Charoensapsri a,b , Nusree Samaluka c , Parichat Chumtong a,b , Patchari Yocawibun a,b , Chanprapa Imjongjirak d,** a Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand b Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand c Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand d Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand ARTICLE INFO Keywords: Transcriptome Betta fish Antimicrobial peptide Immunity ABSTRACT Siamese fighting fish (Betta splendens) is one of the most widely cultivated ornamental fish in global trade. However, transcriptomic data, which can reveal valuable genetic data for disease control and prevention, are extremely limited for this species. In this study, whole-body transcriptome sequencing of juvenile betta fish generated 4.457 GB of clean data and a total of 71,775 unigenes using the Illumina HiSeq4000 platform. These unigenes were functionally classified using 7 functional databases, yielding 45,316 NR (63.14%), 47,287 NT (65.88%), 39,105 Swiss-Prot (54.48%), 16,492 COG (22.98%), 37,694 KEGG (52.52%), 4,506 GO (6.28%), and 35,374 Interpro (49.28%) annotated unigenes. Furthermore, we also detected 13,834 SSRs distributed on 10,636 unigenes and 49,589 predicted CDSs. Based on KEGG analysis, five innate immune pathways (997 unigenes) were reported, including the NOD-like receptor signaling pathway, complement and coagulation cascades, toll- like receptor signaling pathway, RIG-I-like receptor signaling pathway and cytosolic DNA-sensing pathway. Moreover, four antimicrobial peptide (AMP) families (hepcidin, piscidin, LEAP-2, and defensins) from the betta fish transcriptome were also identified. Additionally, cDNA and genomic DNA of two β-defensins was success- fully isolated from four betta fish species. RT-PCR analysis showed that BsBD1 transcripts were most abundant in the muscle and kidney and BsBD2 transcripts were most abundant in the gill. The genomic organization showed that the BD1 and BD2 genes consisted of three exons and two introns according to the GT-AG rule. Most im- portantly, this is the first report of the betta fish whole-body transcriptome obtained by high-throughput se- quencing. Our transcriptomic data and the discovery of betta fish AMPs should promote a better understanding of molecular immunology for disease prevention for further ornamental fish aquaculture. 1. Introduction Siamese fighting fish (Betta splendens) is one of the most popular aquarium fish in the world. In Thailand, B. splendens is a very important ornamental species due to its high economic value from global exports in aquarium fish markets. To date, Siamese fighting fish trade is a de- veloping worldwide industry. More than 50% of betta fish originate from Asian countries, including Thailand. Among the several Betta species, the most well-known is B. splendens (often known as Siamese fighting fish) [1,2]. The expansion of the ornamental fish industry worldwide has caused widespread pathogenic infection, which is a major concern for the sustainable development of betta fish farming. However, despite its commercial importance, little is known about the molecular biology and immune defense of B. splendens. Therefore, studying the transcriptomes of this species is necessary to better un- derstand their molecular biology and immunity. Available tran- scriptomic information could lead to a better understanding of the molecular mechanisms required for betta fish to improve their health and to control diseases in this species. In recent years, increasing oc- currences of diseases in betta fish, such as mycobacteriosis, skin nodule https://doi.org/10.1016/j.fsi.2020.02.030 Received 16 October 2019; Received in revised form 8 February 2020; Accepted 14 February 2020 * Corresponding author. Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. ** Corresponding author. Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand. E-mail addresses: piti.amp@biotec.or.th (P. Amparyup), chanprapa.i@chula.ac.th (C. Imjongjirak). Fish and Shellfish Immunology 99 (2020) 403–413 Available online 17 February 2020 1050-4648/ © 2020 Elsevier Ltd. All rights reserved. T