Marker Gene Sequencing

• 16S rRNA Gene for Bacteria: For bacterial organisms, sequencing the 16S rRNA gene can provide insights into genetic similarity. This gene is highly conserved among bacteria but contains variable regions that can be used to differentiate species.
• COI Gene for Animals: In animals, the cytochrome c oxidase I (COI) gene is commonly used for DNA barcoding and can be used to estimate genetic similarity.

Yes we can calculate similarity based on multilocus sequence analysis (MLSA) or by average nucleotide identity (ANI) based partial genome sequences or selected conserved gene sequences like 16S rRNA for prokaryotes.

Prior to the era of whole genome sequencing, people were estimating similarity using DNA-DNA hybridization.