Final answer:
Complementary DNA (cDNA) is used in RNA sequencing because it captures only the genes that are actually being expressed, it's more stable than RNA, making it less prone to degradation, and current sequencing protocols are predominantly designed for DNA, not RNA.
Step-by-step explanation:
The reason complementary DNA (cDNA) is used in RNA sequencing is multifaceted. To begin with, cDNA captures all the genes expressed in a given tissue or cell, offering a focused view on actual gene expression rather than all potential genetic information coded in the DNA. This is crucial because different cells and tissues express different subsets of their genome at any given time. Furthermore, cDNA has the advantage of being more stable than RNA, making it more practical for experimental manipulation and long-term storage. RNA molecules are inherently unstable due to the widespread presence of RNAses that degrade them. Therefore, using cDNA avoids the technical challenges associated with RNA's instability. Lastly, the existing sequencing protocols and technologies have been primarily developed for DNA sequences. Due to this, constructing cDNA from mRNA templates allows us to harness these protocols effectively. In sum, the use of cDNA enables RNA sequencing to be more accurate, stable, and compatible with existing sequencing technologies.