![]() ![]() Although these powerful and rapidly evolving technologies have only been available for a few years, they are already making substantial contributions to the understanding of genome expression and regulation under different conditions. Next-generation sequencing (NGS) technologies offer the opportunity to generate genome-wide sequence data sets for a reasonable cost and time –. Understanding the transcriptome is essential for interpreting the functional elements of the genome, for revealing the molecular constituents of cells and tissues, and for understanding complex biological processes such as growth, reproduction, and immune response. Major challenges facing transcriptomic research in non-model organisms are increasing the speed and accuracy of discovering new genes and metabolic pathways, as well as determining how gene transcription variations are regulated by specific DNA polymorphisms. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This study was supported by the FONDAP (15110027) project granted by CONICYT-Chile. Received: OctoAccepted: FebruPublished: April 1, 2014Ĭopyright: © 2014 Gallardo-Escárate et al. PLoS ONE 9(4):Įditor: Cynthia Gibas, University of North Carolina at Charlotte, United States of America rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.Ĭitation: Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G (2014) RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi. The data presented in this study provides the most comprehensive transcriptome resource available for C. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. Gene ontology analysis revealed that the nauplius I–II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Herein, four clusters were differentially expressed between nauplius I–II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. ![]() A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. ![]()
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