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

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