Transcriptome analysis of Atlantic Herring (Clupea harengus) using Next Generation Sequencing (NGS)

The Atlantic herring is one of the most abundant fish species in the Northern hemisphere especially in the Northeast Atlantic. There are various stocks of this fish due to their spawning time and their vast distribution. Many studies have tried to characterize herring populations and these efforts can be combined with massively parallel sequencing technologies to develop genetic resources. The transcriptome is a repertoire of RNAs in cells produced by transcription and messenger RNAs (mRNAs) are responsible for gene expression. This repertoire may change during different life stages and environmental conditions. Transcriptome studies have been mainly dependent on a reference genome and developed tools are not applicable for non-model organisms for which the reference genome is missing or only partially available. In this study we present a de novo transcriptome assembly by using different strategies and one specific transcriptome assembler, Trinity. The RNA was collected from muscle of a male spring spawning herring and then sequenced with an Illumina Hiseq 2000 machine. After trimming for low quality nucleotides and possible contaminations, the assembly resulted in 131,788 contigs with a total size of 40 million nucleotides (Mnts). The transcriptome generated by Trinity was compared with other assemblies, assembled by a genome assembler (SOAPdenovo), Inchworm, SSPACE, and CAP3. The results showed that Trinity developed a more reliable assembly. We validated almost 47% of all contigs by comparison to available databases such as nr and other vertebrate transcripts. Also, we quantified the relative expression of transcripts by counting the number of aligned reads per kilobase per million mapped reads (RPKM). Furthermore, we preformed indepth studies of two genes. We identified two copies of Glucose 6-phosphate isomerase (GPI) on draft genome assembly. Our results showed that the sampled fish was heterozygous at the GPIb locus. Among the alpha actin isoforms, we identified the alpha actin b transcript (ACTA1b) in fast muscle corresponding to spring spawning herring fish characteristics