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

Münevver Oral

Article Details

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

Authors:

Münevver Oral

Publisher:

Istanbul University

Main Topics:

Hydrobiology

Journal:

Aquatic Sciences and Engineering Vol.38 Issue 1, pp.1-5

Document Type:

Article

Publication Date:

1/2023

Document Language:

English

Document ID (Org No.):

2001281623

pISSN:

2602-473X

Keywords:

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 interest. 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.

 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 interest. 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.

 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 interest. 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.

 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 interest. 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.

Article Details

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

Authors:

Münevver Oral

Publisher:

Istanbul University

Main Topics:

Hydrobiology

Journal:

Aquatic Sciences and Engineering Vol.38 Issue 1, pp.1-5

Document Type:

Article

Publication Date:

1/2023

Document Language:

English

Document ID (Org No.):

2001281623

pISSN:

2602-473X

Reference genome

genome comparison

brown trout

Salmo trutta

Issues

Article Details

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

Authors: Münevver Oral

Publisher: Istanbul University

Main Topics: Hydrobiology

Journal: Aquatic Sciences and Engineering Vol.38 Issue 1, pp.1-5

Document Type: Article

Publication Date: 1/2023

Document Language: English

Document ID (Org No.): 2001281623

pISSN: 2602-473X

Reference genome

genome comparison

brown trout

Salmo trutta

Issues

Authors:

Münevver Oral

Publisher:

Istanbul University

Main Topics:

Hydrobiology

Journal:

Aquatic Sciences and Engineering Vol.38 Issue 1, pp.1-5

Document Type:

Article

Publication Date:

1/2023

Document Language:

English

Document ID (Org No.):

2001281623

pISSN:

2602-473X