Small subunit ribosomal RNA (rRNA) gene is one of the most widely used phylogenetic markers. Answer the following questions:
1. What are the differences between small subunit rRNA and 16S or 18S rRNA?
2. Obtain the sequence of small subunit rRNA genes of the following organisms. Calculate sequence similarities between them and explain the results.
- Human nuclear small subunit rRNA gene
- Human mitochondrial small subunit rRNA gene
- Mouse nuclear small subunit rRNA gene
- Mouse mitochondrial small subunit rRNA gene
- Nuclear small subunit rRNA gene of any plant species
- Mitochondrial small subunit rRNA gene of any plant species
- Chloroplast small subunit rRNA gene of any plant species
- Small subunit rRNA gene of any bacterial species
- Small subunit rRNA gene of any archaeal species
- You can obtain sequences at https://www.ncbi.nlm.nih.gov/nuccore/. Only the (nearly) full length of the gene should be obtained.
- Various tools can be used to align two or more sequences and calculate sequence similarities. You can easily find them using the Google search. A widely used tool for pairwise alignment is at http://www.ebi.ac.uk/Tools/psa/.
- Small subunit (=SSU) rRNA is called differently for the different domains. For Bacteria and Archaea (Prokaryotes), it is called 16S rRNA. For Eukarya (Eukaryotes), it is called 18S rRNA. Please note that SSU rRNA of mitochondrion and plastid (chloroplast) is also called 16S rRNA. All genes coding SSU (16S or 18S) are homologous, which means that they share a common ancestor. Therefore, you should be able to (roughly) see how they are phylogenetically related by calculating sequence similarities.
Last updated April 24, 2017