| Summary: | The European sardine (Sardina pilchardus) is a fish of high cultural and economic importance in Portugal and current stock assessment studies report an alarming stock biomass decrease due to overfishing and/or environmental change. For better management of the sardine fisheries, there is an urgent need to understand the causal factors leading to the historically low level of the sardine stock in Portuguese waters. Important biological questions such as population diversity level, structure and migrations can be tackled with the development and usage of genomic tools. The ability to answer such important biological questions will be valuable and can be integrated into stock assessment data modelling and aid data-based policy making for better biological resource management. Eleven tissues were sequenced and curated to assemble the transcriptome. Through the comparison of different approaches, the best seemed to go through a quality control step with Trim Galore and a de novo assembly. A post-assembly quality control with Transrate seemed to be better when assembling a group of different tissues rather than one specific ones. The assembly with reads from all the tissues studied contained 170,478 contigs and had an N50 value of 486. Before this project almost no genomic/genetics resources existed to assist biological studies of the sardine and the species genome and transcriptome are cornerstone resources needed to translate applied scientific genetic data into management measures. In this project, a reference transcriptome of the sardine was assembled and functionally annotated.
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