Abstract

Atlantic salmon (Salmo salar) is a major species produced in world aquaculture and an important vertebrate model organism for studying the process of rediploidization following whole genome duplication events (Ss4R, 80 mya). The current Salmo salar transcriptome is largely generated from genome sequence based in silico predictions supported by ESTs and short-read sequencing data. However, recent progress in long-read sequencing technologies now allows for full-length transcript sequencing from single RNA-molecules. This study provides a de novo full-length mRNA transcriptome from liver, head-kidney and gill materials. A pipeline was developed based on Iso-seq sequencing of long-reads on the PacBio platform (HQ reads) followed by error-correction of the HQ reads by short-reads from the Illumina platform. The pipeline successfully processed more than 1.5 million long-reads and more than 900 million short-reads into error-corrected HQ reads. A surprisingly high percentage (32%) represented expressed interspersed repeats, while the remaining were processed into 71 461 full-length mRNAs from 23 071 loci. Each transcript was supported by several single-molecule long-read sequences and at least three short-reads, assuring a high sequence accuracy. On average, each gene was represented by three isoforms. Comparisons to the current Atlantic salmon transcripts in the RefSeq database showed that the long-read transcriptome validated 25% of all known transcripts, while the remaining full-length transcripts were novel isoforms, but few were transcripts from novel genes. A comparison to the current genome assembly indicates that the long-read transcriptome may aid in improving transcript annotation as well as provide long-read linkage information useful for improving the genome assembly. More than 80% of transcripts were assigned GO terms and thousands of transcripts were from genes or splice-variants expressed in an organ-specific manner demonstrating that hybrid error-corrected long-read transcriptomes may be applied to study genes and splice-variants expressed in certain organs or conditions (e.g., challenge materials). In conclusion, this is the single largest contribution of full-length mRNAs in Atlantic salmon. The results will be of great value to salmon genomics research, and the pipeline outlined may be applied to generate additional de novo transcriptomes in Atlantic Salmon or applied for similar projects in other species.

Highlights

  • Atlantic Salmon (Salmo Salar) is a species with significant value both economically and scientifically

  • Two of the head-kidney samples included in the study (SAV_Control and SAV_challenge, Table 1) were from one healthy control fish and one fish challenged with Salmonid Alphavirus, respectively

  • All fish tested negative for SAV3, Infectious salmon anemia virus (ISAV), Infectious pancreatic necrosis virus (IPNV), Piscine myocarditis virus (PMCV), Piscine orthoreovirus (PRV), and Salmon gill poxvirus (SGPV) prior to the challenge trial confirming that the control fish were healthy fish not infected by any of the fish virus commonly seen in aquaculture industry

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Summary

Introduction

Atlantic Salmon (Salmo Salar) is a species with significant value both economically and scientifically. Salmonids have undergone a relatively recent whole genome duplication (WGD) event, (the salmonid-specific fourth vertebrate whole genome duplication, Ss4R) approximately 80 million years ago (Allendorf and Thorgaard, 1984; Macqueen and Johnston, 2014) They are undergoing rediploidization, which makes Atlantic salmon a model species useful for studying post WGD phenomena like rediploidization and conservation of partial tetrasomy (Lien et al, 2016; Campbell et al, 2019). High-quality transcriptomic resources are extremely valuable when studying the underlying molecular processes governing such developmental transformations, molecular details of infectious diseases as well as in the study of the post WGD phenomena They are very important resources for the continuing knowledge-based aquaculture management to improve fish welfare and ensure growth of the aquaculture industry (Abdelrahman et al, 2017)

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