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Hongo, Jorge Augusto, et al. “CALANGO: A Phylogeny-Aware Comparative Genomics Tool for Discovering Quantitative Genotype-Phenotype Associations across Species.” Patterns, Apr. 2023, p. 100728, https://doi.org/10.1016/j.patter.2023.100728.
Name a few organisms you can think of. Do they all look the same? Or are they varied? This variation of life is a product of the genome.
A genome is the entire set of DNA instructions that are present in every cell of a living organism. This DNA codes for proteins that define things like our hair, eyes, and other physical characteristics. Within the genome of a species, there may also be variations. For example, you may have brown eyes but someone else may have black, green, or blue eyes. This is due to a difference in the genotype. Genotype refers to the unique sequence of DNA that an individual possesses. These genotypes are expressed as visible characteristics (such as eye colour). The visible expression of the genotype is called the phenotype.
Due to evolution, the genomes of organisms have developed to create a vast and diverse range of species. Genome content can be as diverse in terms of the length of DNA and its composition. Due to this evolution of species from common ancestors and the genetic diversity, it becomes hard for researchers to understand the processes that the genome undergoes that can be associated with the development of differences between species. Furthermore, there is an obstacle in the integration and analysis of genetic data in a meaningful manner and within a comparative evolutionary framework.
Due to developments in research, biologists now have access to large amounts of phenotypic and genomic data for certain species and can move on to developing relationships between known genes and phenotypes. This research paper introduces CALANGO. CALANGO is a tool that can use comparison to search for genome associations between genotypes and phenotypes across species. This tool is also aware of the evolutionary relationships between species. Therefore it overcomes one of the main obstacles in investigating the genome - since species share common ancestors, certain genes are not exclusively linked to one species.
The research paper demonstrates the use of CALANGO in two case studies where it explores both known and unknown phenotype and genotype associations in E. Coli and angiosperms. The discoveries from just these two studies can have implications for conservation biology and agriculture.
CALANGO is a useful tool and one of the first that uses known evolutionary relationships between species to investigate the genotypic and phenotypic associations present in organisms. It uses statistical methods and testable hypotheses that can lead to breakthroughs in our understanding of complex genetic diseases and genetic breeding. Researchers can block certain genes to allow CALANGO to form a causal relationship between a specific gene and phenotype; however, future developments could lead to the creation of a tool that specifically models these causal relationships. For now, CALANGO has filled a gap in the genomics field and furthered our understanding of the genome.
Works Cited
“Genotype and Phenotype.” Garvan Institute of Medical Research, 2021, www.garvan.org.au/research/kinghorn-centre-for-clinical-genomics/learn-about-genomics/for-gp/genetics-refresher-1/genotype-and-phenotype. Accessed 30 May 2023.
Green, Eric. “Genome.” Genome.gov, 25 May 2023, www.genome.gov/genetics-glossary/Genome. Accessed 30 May 2023.
ScienceDaily. “Software to Untangle Genetic Factors Linked to Shared Characteristics among Different Species.” ScienceDaily, 14 Apr. 2023, www.sciencedaily.com/releases/2023/04/230414201831.htm. Accessed 30 May 2023.
“What Is Phylogeny?- Ontogeny & Phylogeny.” BYJUS, byjus.com/biology/phylogeny/. Accessed 30 May 2023.
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