Salmobase

Salmobase provides an integrated visual and analytic framework for molecular genomic resources of salmonid species, focusing on Atlantic salmon (Salmo salar) and rainbow trout, to support genomic and evolutionary analyses.

Key Features:

• Integrated Data Access: Access to genome sequences and related data via BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse), and Gene Expression Browser (GEBrowse).
• Evolutionary Insights: Resources and data for studying the whole‑genome duplication (WGD) ~80 million years ago that produced an autotetraploid ancestor and the subsequent rediploidization process.
• Comparative Genomics Tools: Synteny browsers and comparative genomics tools for analyzing gene retention, expression patterns, genomic reorganizations, and transposon‑mediated repeat expansions across salmonids.
• Gene Expression Analysis: Examination of duplicate gene expression across tissues to evaluate neofunctionalization versus subfunctionalization, including comparisons with orthologous genes from pre‑WGD outgroups.
• Reference Genome Utility: Use of the high‑quality Atlantic salmon (Salmo salar) genome assembly as a reference for studying other salmonid genomes across the ~70 extant lineages in Salmonidae.

Scientific Applications:

• Whole‑genome duplication studies: Investigation of the evolutionary consequences of WGD and ongoing rediploidization in Salmonidae.
• Vertebrate genomics: Analysis of genomic architecture and mechanisms of gene retention and loss following duplication events.
• Comparative genomics across Salmonidae: Cross‑species analyses of synteny, gene organization, and genomic rearrangements among salmonid lineages.
• Gene expression evolution: Studies of duplicate gene expression divergence and functional evolution across tissues and species.
• Applied fisheries genomics: Support for genomic research relevant to fisheries science using salmonid genomic resources and comparative reference data.

Methodology:

Provides BLAST, GBrowse, GVBrowse, GEBrowse, synteny browsers and comparative genomics tools built around the Atlantic salmon reference genome assembly.