Using the NIH Comparative Genomics Resource (CGR) to gain knowledge about less-researched organisms
The scientific community relies heavily on model organism research to gain knowledge and make discoveries. However, focusing solely on these species misses valuable variation. Comparative genomics allows us to use knowledge from a model species, such as Saccharomyces cerevisiae, to understand traits in other, related organisms, such as Saccharomyces pastorianus or Saccharomyces eubayanus. Applying this information may provide valuable insight for other less-researched organisms. The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help you do just that.
How and why should you use our resources? Consider the example below.
Yeast has been used in beer brewing and bread baking for millennia. The specific species of yeast (Saccharomyces cerevisiae) traditionally used to make beer, bread, and wine has been cultured and domesticated over time as a distinct species from other environmental yeasts.
Researchers used comparative genomics methods to uncover the origin of the yeast strain involved in lager-style beer production, Saccharomyces pastorianus (PMC316705). They found that this organism was likely created by fusion of S. cerevisiae and the cold-hardy yeast, Saccharomyces eubayanus.
In addition to the ability to thrive in cold temperatures, S. pastorianus is also better able to use some of the recipe’s barley malt sugars than S. cerevisiae. Leftover malt sugars are often used as a biomarker to differentiate between these two yeast species.
The following are relevant CGR and other NCBI resources that facilitate comparisons between the well known S. cerevisiae (Ale-style beer & bread yeast), and the lesser-studied S. pastorianus (Lager-style beer yeast) or S. eubayanus (cold-tolerant yeast) – from whole genome alignments down to the protein structure of the specific IMA1 sugar-metabolizing gene:
|Find available genome data for S. cerevisiae and S. pastorianus or S. eubayanus with NCBI Datasets|
|Compare genomes of S. cerevisiae & S. pastorianus or S. pastorianus & S. eubayanus using the Comparative Genome Viewer (CGV)|
|Explore the alignment of the S. cerevisiae & S. pastorianus IMA1 sugar-metabolizing genes with the Multiple Sequence Alignment (MSA) Viewer|
|Identify sequence-level differences and conserved domains in the IMA1 sugar-metabolizing gene with the Genome Data Viewer (GDV)|
|Learn more about the largest functional domain in the IMA1 protein in Conserved Domain Database (CDD)|
|Use RefSeq protein sequence to find all sequences similar to IMA1 in the S. pastorianus genome using BLAST, and use Tree View to visualize their relatedness|
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