Which of the following RNA is commonly used for phylogenetic analysis ?

Question

Accepted Answer

The correct option is 1: 16 S rRNA

The 16S ribosomal RNA (rRNA) gene is universally recognized as the "gold standard" molecular marker for phylogenetic analysis, particularly in prokaryotic organisms (Bacteria and Archaea). The reason for its common use lies in its unique set of characteristics perfectly suited for evolutionary comparisons. First, the gene for 16S rRNA is ubiquitous, meaning it is present in all bacterial and archaeal species because it codes for an essential component of the 30S (small) ribosomal subunit necessary for protein synthesis. Second, the gene is approximately 1,500 base pairs long, which is a moderate, manageable length for sequencing, but critically, its sequence is a mosaic of highly conserved regions and nine hypervariable regions (V1-V9). The conserved regions allow scientists to design universal primers to amplify the gene from any prokaryotic DNA sample, while the variable regions contain enough genetic differences (phylogenetic information) to accurately resolve evolutionary relationships from the phylum level all the way down to the species level. This combination of universality, conserved structure, and resolving power has led to the creation of vast, publicly accessible sequence databases, solidifying 16S rRNA’s role as the primary tool for microbial identification and evolutionary studies.

The incorrect option is 2: 5 S rRNA

The 5S rRNA is a constituent of the large ribosomal subunit, and like the 16S rRNA, it is universally distributed across all domains of life. However, it is a very small RNA molecule, typically only about 120 nucleotides in length. Because of its significantly smaller size compared to the 16S rRNA gene (approximately 1,500 nucleotides), the 5S rRNA gene contains far fewer informative variable regions. This lack of sequence variation limits its phylogenetic resolution, meaning it cannot reliably distinguish between closely related species or genera. While it was used in early molecular evolution studies due to the ease of sequencing small molecules, it was quickly superseded by the more information-rich 16S rRNA for routine phylogenetic analysis.

The incorrect option is 3: 28 S rRNA

The 28S rRNA is the major component of the large ribosomal subunit (60S) in eukaryotes, making it the counterpart to the prokaryotic 23S rRNA. While ribosomal RNA is generally useful for phylogeny, the 28S rRNA gene is substantially larger than the 16S rRNA, and its size can vary significantly across different eukaryotic groups due to the presence of large "expansion segments." This high variability in both length and structure makes universal primer design and standardized PCR amplification—which are key requirements for common, high-throughput analysis—extremely difficult. Furthermore, 16S rRNA is the standard for the vast and diverse field of microbial ecology and taxonomy, which focuses primarily on the prokaryotic domains.

The incorrect option is 4: hn RNA

The term hnRNA stands for heterogeneous nuclear RNA, which is the precursor or unprocessed form of messenger RNA (mRNA) found only within the nucleus of eukaryotic cells. hnRNA is highly unstable and is immediately processed by splicing, capping, and tailing before it becomes mature mRNA. Because it is a transient intermediate molecule that is not universally conserved and whose sequence changes depending on the protein it codes for, it lacks the two most critical qualities required for a phylogenetic marker: stability and universal presence across a broad taxonomic range. Therefore, hnRNA cannot be used to compare or infer the evolutionary relationships between different organisms.