Horizontal gene transfer MCQs With Answer

Horizontal gene transfer (HGT) is the non-vertical movement of genetic material between organisms and plays a central role in the spread of antibiotic resistance, metabolic traits, and virulence determinants. This quiz-focused blog presents 20 targeted MCQs with answers designed for M.Pharm students studying Bioinformatics and Computational Biotechnology. Questions cover mechanisms — transformation, conjugation, generalized and specialized transduction — and mobile elements like plasmids, transposons, integrons, and genomic islands. Emphasis is placed on detection strategies, genomic signatures of HGT, experimental assays, clinical implications, and bioinformatic tools used to infer lateral transfer events. Use these MCQs to test conceptual understanding, prepare for exams, and appreciate HGT’s pharmaceutical and public-health relevance.

Q1. Which mechanism of horizontal gene transfer requires uptake of naked DNA from the environment by a competent bacterial cell?

• Conjugation via plasmid-encoded pili
• Transformation by natural competence
• Generalized transduction by bacteriophages
• Transposition via insertion sequences

Correct Answer: Transformation by natural competence

Q2. Conjugative plasmids commonly transfer genes between bacteria through which structure?

• Type IV secretion system (pilus-mediated mating pair formation)
• Flagellar rotation pump
• Nucleoid exchange channels
• Outer membrane vesicles only

Correct Answer: Type IV secretion system (pilus-mediated mating pair formation)

Q3. Which form of transduction transfers random fragments of host DNA packaged by a bacteriophage?

• Specialized transduction
• Generalized transduction
• Conjugational transduction
• Transformation-linked transduction

Correct Answer: Generalized transduction

Q4. Integrons are important in antibiotic resistance because they primarily function to:

• Encode conjugative pili for plasmid transfer
• Capture and express gene cassettes including resistance genes via integrase-mediated recombination
• Increase mutation rates globally in the genome
• Form double-stranded DNA breaks to facilitate recombination

Correct Answer: Capture and express gene cassettes including resistance genes via integrase-mediated recombination

Q5. A genomic signature often used to detect recent HGT events in a bacterial genome is:

• High conservation of operon structure with close relatives
• Marked deviation in GC content and codon usage compared to host genome
• Presence of abundant ribosomal RNA genes
• Uniform mutation spectrum across the chromosome

Correct Answer: Marked deviation in GC content and codon usage compared to host genome

Q6. Mobile genetic elements that can move within and between genomes using a “cut-and-paste” mechanism are called:

• Plasmids
• Transposons
• Integrative conjugative elements (ICEs)
• Bacteriophages

Correct Answer: Transposons

Q7. Which bioinformatic approach is most appropriate to infer horizontal gene transfer for a specific gene across species?

• Comparative phylogenetic analysis showing discordant gene tree vs species tree
• Counting the number of single nucleotide polymorphisms (SNPs) only
• Measuring RNA expression level under stress conditions
• Calculating protein isoelectric point distributions

Correct Answer: Comparative phylogenetic analysis showing discordant gene tree vs species tree

Q8. Which restriction-modification system in bacteria acts as a barrier to incoming foreign DNA and thereby limits HGT?

• CRISPR-Cas adaptive immune systems exclusively
• Methylation-sensitive restriction endonucleases that degrade unmethylated foreign DNA
• Type IV pili assembly proteins
• Transposase-mediated DNA integration

Correct Answer: Methylation-sensitive restriction endonucleases that degrade unmethylated foreign DNA

Q9. Specialized transduction differs from generalized transduction because specialized transduction:

• Packages random host DNA fragments of any genomic location
• Transfers only specific host genes adjacent to prophage integration sites
• Requires conjugative plasmids as intermediates
• Occurs only between distantly related species

Correct Answer: Transfers only specific host genes adjacent to prophage integration sites

Q10. Which experimental method can directly demonstrate plasmid-mediated conjugation between two bacterial strains?

• Filter mating assay with selection for transconjugants
• PCR amplification of 16S rRNA genes only
• Northern blot for plasmid-encoded mRNA
• Restriction fragment length polymorphism of chromosomal DNA

Correct Answer: Filter mating assay with selection for transconjugants

Q11. Integrative conjugative elements (ICEs) differ from plasmids because ICEs:

• Exist only as extracellular DNA molecules
• Integrate into the host chromosome and can excise to transfer by conjugation
• Are always non-self-transmissible and require helper plasmids
• Encode only antibiotic resistance genes without transfer functions

Correct Answer: Integrate into the host chromosome and can excise to transfer by conjugation

Q12. A pathogen acquires a toxin gene via HGT that is flanked by insertion sequences; the most likely mechanism is:

• Transformation of a chromosomal fragment lacking mobile elements
• Transposition mediated by transposons or insertion sequences
• General mutation and selection without horizontal transfer
• Specialized transduction by a virus targeting ribosomal genes

Correct Answer: Transposition mediated by transposons or insertion sequences

Q13. In a genomic epidemiology context, rapid spread of the same resistance plasmid across multiple clinical isolates is best explained by:

• Vertical inheritance from a common ancestor only
• Horizontal transfer of a conjugative plasmid between strains
• Independent point mutations creating identical resistance alleles
• Loss of plasmids in all isolates simultaneously

Correct Answer: Horizontal transfer of a conjugative plasmid between strains

Q14. Which computational signature is LEAST informative for identifying HGT events in prokaryotic genomes?

• Phylogenetic incongruence between gene and species trees
• Marked local GC content deviation
• Presence of flanking direct repeats or mobility genes
• High conservation of ribosomal protein gene sequences

Correct Answer: High conservation of ribosomal protein gene sequences

Q15. Bacterial natural competence is regulated and typically induced by:

• Constitutive expression in all growth conditions
• Environmental signals such as nutrient limitation, cell density, or stress
• Direct infection by conjugative plasmids only
• Exposure to UV light exclusively

Correct Answer: Environmental signals such as nutrient limitation, cell density, or stress

Q16. Which of the following is a common consequence of HGT in clinical settings?

• Reduction in pathogenicity due to gene loss only
• Rapid dissemination of antibiotic resistance and virulence determinants
• Complete stabilization of host genome GC content
• Elimination of mobile genetic elements from all bacteria

Correct Answer: Rapid dissemination of antibiotic resistance and virulence determinants

Q17. The pan-genome concept relates to HGT because:

• It describes only the conserved core genome and ignores accessory genes
• Accessory genes acquired by HGT contribute to the variable part of the pan-genome
• It limits gene transfer between species by sequence homology
• Pan-genomes are identical across all strains of a species

Correct Answer: Accessory genes acquired by HGT contribute to the variable part of the pan-genome

Q18. Which mobile element is best known for mediating multi-gene antibiotic resistance cassettes and often associates with transposons and plasmids?

• Ribosomal RNA operons
• Integrons
• CRISPR arrays
• Origin of replication (oriC)

Correct Answer: Integrons

Q19. In metagenomic datasets, a practical indicator suggesting HGT between taxa is:

• Finding identical short reads mapping to conserved housekeeping genes only
• Assembling contigs that contain genes with best BLAST hits to distantly related taxa and mobile-element markers
• Uniform coverage depth across all contigs
• Exclusive detection of single-copy core genes

Correct Answer: Assembling contigs that contain genes with best BLAST hits to distantly related taxa and mobile-element markers

Q20. Which tool or approach is specifically designed to reduce false positives when predicting HGT by integrating phylogenetic and compositional evidence?

• Simple BLAST best-hit annotation without phylogenetics
• Combined pipelines such as HGTector or DarkHorse that integrate phylogenetic profiling and compositional filters
• Counting ORFs per contig only
• Using GC skew plots exclusively

Correct Answer: Combined pipelines such as HGTector or DarkHorse that integrate phylogenetic profiling and compositional filters

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