Divergence of cochlear transcriptomics between reference‑based and reference‑free transcriptome analyses among...

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Gene expression differences drive tissue function and phenotypic divergence.
• Transcriptome analysis is crucial for understanding molecular mechanisms.
• Reference-based and reference-free methods are two main approaches for transcriptome analysis.

Purpose of the Study:

• To compare reference-based and reference-free transcriptome analysis methods.
• To evaluate their effectiveness in analyzing the cochlear transcriptome of greater horseshoe bats with different acoustic phenotypes.
• To provide insights into selecting appropriate transcriptome analysis strategies.

Main Methods:

• Comparative analysis of transcriptome data from three greater horseshoe bat lineages.
• Application of both reference-based and reference-free transcriptome analysis techniques.
• Evaluation of accuracy, reliability, and annotation rates of each method.

Main Results:

• Reference-based methods demonstrated lower false-positive rates and higher accuracy.
• Differentially expressed genes identified via reference-based methods showed greater reliability and annotation rates.
• Phenotype-related terms (inorganic molecules, proton channels) were identified exclusively by the reference-based method.
• Reference-based methods may have limitations in information acquisition.

Conclusions:

• Reference-based transcriptome analysis provides more accurate and reliable results for gene expression studies.
• A combined approach utilizing both reference-free and reference-based methods is ideal for comprehensive transcriptome analysis.
• This study offers guidance for selecting optimal transcriptome analysis methods in future research.