The genomic build for rainbow trout (Oncorhynchus mykiss) has recently been released on NCBI (May 2017). We are currently working with other researchers on the completion of a genomic build for Arctic charr (Salvelinus alpinus). Oncorhynchus and Salvelinus are sister clades in the teleost family Salmonidae, and represent one of the lineages in teleost fishes that have undergone and additional whole genome duplication (4R WGD). The duplication in the stem ancestor to salmonids represents a 4th round of WGD in addition to the 3rd round which occurred in the stem ancestor of the teleost fishes (3R WGD). As such, salmonids represent an excellent vertebrate model group in which to study the consequences of WGD on gene arrangements, retention of duplicates, and organization of the genome into functional units. Projects in the lab may involve one of the following aspects, but are by no means restricted to this list.
- Assessment of functional Gene Ontology groupings within syntenic chromosome blocks and assessment of the retention of WGD paralogues.
- Assessment of GC content variation across the genomes which may relate to recombination hotspots.
- Reassessment of transcriptomic data collected in the lab and other sources related to growth differences and stress tolerance (salinity and thermal stress tolerance) with the objective of aligning reads to specific duplicate gene copies that occur on the 4R duplicated chromosome arms.