Genomics/Technical resource papers Characterization of the growth-related transcriptome in California red abalone (Haliotis rufescens) through RNA-Seq analysis Diego Valenzuela-Miranda a , Miguel A. Del Río-Portilla b, ⁎, Cristian Gallardo-Escárate a, ⁎ a Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR) Department of Oceanography, University of Concepción, P.O. Box 160-C, Chile b Laboratorio de Genética, Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada No 3918, C.P. 22860 Ensenada, BC, Mexico abstract article info Article history: Received 24 March 2015 Received in revised form 11 May 2015 Accepted 12 May 2015 Available online xxxx Keywords: RNA-Seq Haliotis Growth Transcriptome One of the largest detriments in the abalone aquaculture industry is the inherently low growth rate of this marine gastropod. In order to confront this issue, greater molecular knowledge is needed on growth traits. Therefore, transcriptome analyses were performed using RNA-Seq for groups of California red abalones (Haliotis rufescens) cultured under the same conditions, but with high growth rates (HGR) or low growth rates (LGR). De novo assembly generated 44312 contigs used as references for RNA-Seq analysis. Results showed a total of 1437 differ- entially expressed contigs, among which, 435 were up-regulated in the HGR group and 1002 in LGR individuals. Overall, LGR abalones evidenced a greater number of exclusive transcripts and differentially transcribed genes. These results provide a valuable resource of novel transcripts in this species and further understandings of the molecular bases regulating growth traits in H. rufescens. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Abalones (Haliotis spp.) are marine gastropods known for their high commercial value worldwide. This economic importance has led to intensive capturing pressures, consequently depleting the stock of wild populations. Due to this, aquaculture has become an alternative for the production and conservation of this marine resource (Diana, 2009). Of the abalone species, the red abalone (Haliotis rufescens) is the larg- est species of abalone worldwide. Thus, their aquaculture industry has evidenced continuous growth due to the adaptability of H. rufescens to culture technologies, its high commercial value and one of the best meat to shell ratios among abalones. However, one of the main disadvantages in abalone aquaculture is the low growth rates inherent to this marine gastropod. Several external factors have been associated with the regulation of growth in abalones, such as temperature, dissolved oxygen, and ammonia (Harris et al., 1998, 1999; Steinarsson and Imsland, 2003). However, the molecular factors that orchestrate growth traits in H. rufescens are not well understood. In recent years, transcriptome sequencing (RNA-Seq) has facilitated the discovery of novel transcripts and the molecular bases underpinning several traits of interest, such as growth traits in Salmo salar (Salem et al., 2012). Based on this, H. rufescens grown under the same physico- chemical conditions were classified according to growth performance (low and high growth rates), and RNA-Seq analysis was conducted fo both groups. The results provided a list of differentially expressed transcripts associated with both conditions, as well as generating the first reference database that can be used to explore and gain a better understanding of the molecular machinery involved in H. rufescens growth. 2. Data description 2.1. RNA isolation and sequencing H. rufescens individuals from the same population were cultured for six months and fed and maintained under the same physicochemical conditions. Growth was monitored, and individuals were qualified in low growth rate (LGR) and high growth rate (HGR) groups according to body weight gain (Fig. 1). After the culturing period, muscle was isolated from 10 individuals in both groups, and RNA isolation was performed using the TRIZOL reagent (Invitrogen) and manufacturer pro- tocol. RNA purity and integrity were checked with a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific) and 2200 TapeStation Marine Genomics xxx (2015) xxx–xxx ⁎ Corresponding authors. E-mail addresses: mdelrio@cicese.mx (M.A. Del Río-Portilla), crisgallardo@udec.cl (C. Gallardo-Escárate). MARGEN-00331; No of Pages 4 http://dx.doi.org/10.1016/j.margen.2015.05.009 1874-7787/© 2015 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Please cite this article as: Valenzuela-Miranda, D., et al., Characterization of the growth-related transcriptome in California red abalone (Haliotis rufescens) through RNA-Seq analysis, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.009