Characterization and Comparative Analysis of MicroRNAs in 3 Representative Red Algae

Area of Science:

• Marine Biology
• Genomics
• Molecular Evolution

Background:

• MicroRNAs (miRNAs) are crucial post-transcriptional gene regulators.
• Previous work identified miRNAs and targets in three red algae species: *Chondrus crispus*, *Galdieria sulphurariais*, and *Porphyridium purpureum*.

Purpose of the Study:

• To perform unique molecular and evolutionary characterization of miRNAs in three red algae species.
• To understand the role of miRNAs in red algal gene expression and biological processes.

Main Methods:

• Comparative miRNA profiling and bioinformatics analysis.
• Genome-wide collinearity analysis of small RNAs (sRNAs), miRNAs, and precursor miRNAs (MIRs).
• Phylogenetic and evolutionary analysis, miRNA target validation (RLM-RACE PCR), and functional enrichment analysis (GO, KEGG).

Main Results:

• Analysis revealed quantity, nucleotide bias, and common sequences of miRNAs across the three red algae.
• Genome-wide distribution and interrelation of sRNAs, miRNAs, and MIRs were determined.
• Evolutionary analysis of miR156 and pre-miR156 showed steady processes under negative selection.
• Cleavage was confirmed as the primary miRNA target inhibition mechanism.
• Enrichment analysis identified significant pathways related to plastid formation and general metabolism.

Conclusions:

• MiRNAs are essential regulators of diverse biological processes in red algae.
• Comprehensive molecular and evolutionary insights into red algal miRNAs can aid in leveraging algae resources at a molecular level.