Scientists have discovered a new marine bacterial species called Vibrio nuigii. They have isolated ten strains of this bacterium and determined their whole genome sequences. Only one of the strains (which the scientists named Vir1) is virulent and causes disease in oysters. Describe three ways in which the scientists could use their knowledge of the bacterial genome sequences to identify the genes responsible for virulence.

1-by transfecting small interfering RNAs against target genes of interest

2-by using comparative genomics strategies in order to infer functional relationships among target genes of interest and homologous genes responsible for virulence in other bacteria (e.g., antibiotic resistance genes)

3- by inducing mutations through site-directed mutagenesis in order to study gene function (i.e., by examining the effects of knockout mutations)

Explanation:

Whole-genome sequencing (WGS), also known as complete genome sequencing, refers to Next Generation Sequencing technologies that allow the obtention of the entire genetic sequence of an organism/cell, which can be used as a reference genome to understand gene function, evolutionary relationships, etc. The information provided by WGS technologies allows making many different types of genetic analyses in order to understand gene function. First, the nucleotide reference sequence can be used to design complementary small interfering RNAs that trigger degradation of target messenger RNAs (mRNAs) by the RNA interference (RNAi) pathway, thereby inhibiting gene function (in this case, inhibiting genes associated with virulence in the bacterial strain). Second, a reference genome is required to perform bioinformatic data analyses in order to identify homologous genes associated with virulence in evolutionarily related bacteria, allowing identify, for example, antibiotic resistance genes or sequence polymorphisms (e.g., single nucleotide polymorphisms, SNPs) associated with gene function. Third, the information provided by a reference genome can also be used to trigger site-directed mutagenesis (for example, by using the highly precise CRISPR-Cas9 genome editing technology) in order to knock out specific genes of interest and thus analyze if the bacterial strain is still infectious.