This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
Genetic Homology and Its Importance
If two things are homologous, it means they share a common ancestor. Thus, genetic homology refers to a gene/genes that are found in different species and originated from a common ancestor [1]. The term homology what originally coined in the 19th century by Robert Owen, a British comparative anatomist. He used this general term to refer to the similarities between certain structures in different organisms, such as the forelimbs of various vertebrates. It was Charles Darwin who later suggested these similarities were due to a common ancestor [2].
The information gained through the study of homology can be extremely useful as it helps us understand how species are related. Homology can be used to help create phylogenetic or evolutionary trees (for more on this see the phylogeny page) [1]. Discovering homologous genes in simpler organisms also enables us to study these genes in model organisms, such as mice or flies, to attempt to determine how they function in humans. This can be crucial for disease discovery and treatment. |
Homologs of the TOP3B Gene
The following genetic homologs for the human TOP3B gene were found using BLAST (Basic Local Alignment Search Tool), an online database of gene and protein sequences that uses a sophisticated algorithm to compare sequences between organisms. I simply entered the accession code for the human gene into a nucleotide blast and selected the organisms that I wanted to search for. BLAST then provided me with a list of homologous genes in those organisms, along with percentages, called 'percent identical,' which refer to the extent to which two sequences have the same nucleotide base at the same position, or how similar the sequences are [3]. The database also presented an Expect (E) value for each percentage; an E value closer to zero means that that number is significant [1].
Analyzing the TOP3B Homologs
All of these homologs have very high 'percent identical's with the human gene. This was expected, however, due the essential function of the topoisomerase protein. Likewise, topoisomerase genes are known to be very highly conserved evolutionarily. The order from 99% identical to 71% identical is rather logical as well. Among these organisms, the chimp is our closest evolutionary relative. Giant pandas, mice, rats, and chickens are all vertebrates, so it is logical that their genetic sequence for TOP3B would be very similar following chimpanzees. The high level of similarity in mice, rats, zebrafish, flies, and worms is also significant because these are widely used model organisms for studying molecular and genetic processes as well as disease progression and treatment. I think the most interesting part is how well conserved this gene is between humans and the two plants listed here, arabidopsis and rice. This verifies how essential this gene is to life, as it is one of the key players in accessing the genetic material.
Below is a list of TOP3B homologs as well as related information. The FASTA link will take you to a page with the DNA sequence of that homolog, which was obtained from the nucleotide database of NCBI.
Below is a list of TOP3B homologs as well as related information. The FASTA link will take you to a page with the DNA sequence of that homolog, which was obtained from the nucleotide database of NCBI.
1. Mus musculus (mouse)-TOP3B (mRNA)
87% identical 0% gaps 0.0 E Accession code: NM_011624.2 FASTA 2. Rattus Norvegicus (rat)-TOP3B (mRNA) 87% identical 0% gaps 0.0 E Accession code: NM_001105861.1 FASTA 3. Gallus gallus (chicken)-TOP3B (mRNA) 77% identical 0% gaps 0.0 E Accession code: NM_001006181.1 FASTA 4. Drosophila melanogaster (fly)- TOP3B (mRNA) 71% identical 2% gaps 3E-39 E Accession code: NM_078504.3 FASTA 5. Caenorhabditis elegans (worm)-Protein Y48C3A.14 (MRNA) 80% identical 0% gaps 1E-28 E Accession code: NM_001267453.1 FASTA |
6. Danio rerio (zebrafish)-TOP3B/LOC793414 (mRNA)
76% identical 1% gaps 0.0 E Accession code: XM_003198603.2 FASTA 7. Pan Trogolodyes (chimp)-TOP3B (mRNA) 99% identical 0% gaps 0.0 E Accession code: XM_003317124.1 FASTA 8. Ailuropoda melanoleuca (Giant panda)- TOP3B (mRNA) 91% identical 0% gaps 0.0 E Accession code: XM_002931107.1 FASTA 9. Arabidopsis Thaliana (plant)-DNA Topoisomerase type 1A (mRNA) 75% identical 0% gaps 1E-11 E Accession code: NM_128760.3 FASTA 10. Oryza Sativa (rice)-Os09g0500600 (mRNA) 76% identical 0% gaps 8E-13 E Accession code: NM_001070113.2 FASTA |
References
[1] Delsuc, F., Brinkmann, H., Philippe, H. Phylogenomic and the reconstruction of the tree of life. Nat Rev Genet. 2005 May; 6(5):361-75.
[2] National Center for Science Education. What is Homology? Created Oct. 2008. Retrieved Feb. 2014. http://ncse.com/evolution/science/what-is-homology
[3] Jan Fassler, Ph.D. and Peter Cooper, Ph.D. NCBI. BLAST Glossary. Created July, 2011. Retrieved Feb. 2014. http://www.ncbi.nlm.nih.gov/books/NBK62051/
[2] National Center for Science Education. What is Homology? Created Oct. 2008. Retrieved Feb. 2014. http://ncse.com/evolution/science/what-is-homology
[3] Jan Fassler, Ph.D. and Peter Cooper, Ph.D. NCBI. BLAST Glossary. Created July, 2011. Retrieved Feb. 2014. http://www.ncbi.nlm.nih.gov/books/NBK62051/