RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

Abstract

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. 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. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. 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. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. 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). 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. 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. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

“…Therefore, the observed changes occurred rapidly and had to rely either on a sufficiently large standing genetic variation of both host and parasite populations or on more plastic mechanisms like gene regulation. Similar to many other nonmodel organism transcriptome studies (e.g., Gallardo‐Escárate, Valenzuela‐Muñoz, & Nuñez‐Acuña, ; Patnaik et al., ; Qi et al., ; Yarra, Gharbi, Blaxter, Peck, & Clark, ), a significant proportion of assembled contigs could not be functionally annotated and we are aware that we may have missed novel functional aspects of co‐evolutionary interactions. Our results based on homology annotation revealed that the direct interaction between host and parasites can generate specificity of general responses (ROS pathways) on the transcription level within few generations, illustrating the value of invasive species for the study of host–parasite co‐evolution in nature.…”

In silico transcriptome analysis of cuticle-related genes associated with delousing drug responses in the sea louse Caligus rogercresseyi

“…Observations in distinct species of insects have shown that variations in cuticle thickness have a significant effect on susceptibility to insecticides (Vannini et al, 2014). Considering this, the present study was performed to determine if exposition to the antiparasitics azamethiphos and deltamethrin modulated transcriptional activity in C. rogercresseyi, with analysis focused on 479 contigs with high homology to genes involved in cuticle formation and identified through previously constructed genomic databases (Gallardo-Escárate et al, 2014).…”

“…From the EST-database reported by Gallardo-Escárate et al (2014) for C. rogercresseyi, 63,444 high quality contigs were annotated according to Gene Ontology terms with the Blast2GO software (Conesa et al, 2005). Furthermore, tBLASTx analysis was performed against ESTdatasets downloaded from the NCBI for cuticle-related sequences reported for arthropod species.…”

“…Cuticle formation-related genes were identified from the C. rogercresseyi database (Gallardo-Escárate et al, 2014), and additionally the identification were performed from EST-database of C. rogercresseyi exposed to azamethiphos and deltamethrin (Valenzuela-Muñoz et al, 2015). From tBlastx analysis, 479 contigs were annotated as genes related to cuticle formation.…”

The race between host and sea lice in the Chilean salmon farming: a genomic approach

“…However, it was not until 2014 that Gallardo‐Escárate et al . () revealed the complete transcriptome modulation occurring in the copepod during ontogenetic development, highlighting several key features of the C. rogercresseyi life cycle that was previously unknown (Table ). The same study also revealed for the first time fundamental molecular differences between male and female adults, information that was only available at the time with EST collections for L. salmonis .…”