What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout

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ORAL M.

Aquatic Science and Engineering, vol.38, no.1, pp.1-6, 2022 (ESCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 38 Issue: 1
  • Publication Date: 2022
  • Doi Number: 10.26650/ase202221172568
  • Journal Name: Aquatic Science and Engineering
  • Journal Indexes: Emerging Sources Citation Index (ESCI), Scopus, TR DİZİN (ULAKBİM)
  • Page Numbers: pp.1-6
  • Keywords: Reference genome, genome comparison, brown trout, Salmo trutta, SEQUENCE
  • Recep Tayyip Erdoğan University Affiliated: Yes

Abstract

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific in- terest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta.