Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa

Area of Science:

• Molecular Biology
• Genomics
• Evolutionary Biology

Background:

• Ciliated protozoa (ciliates) are unicellular eukaryotes crucial as model organisms in molecular biology.
• Analyzing codon usage bias (CUB) in ciliate macronuclear (MAC) genomes offers insights into genetic mechanisms and evolutionary trajectories.
• Optimizing codons can enhance gene editing efficiency in these model organisms.

Purpose of the Study:

• To investigate codon usage bias in the macronuclear genomes of 21 ciliate species.
• To identify the primary factors influencing codon usage bias, including mutation and natural selection.
• To provide a foundation for improving gene editing techniques in model ciliates.

Main Methods:

• Calculation of key indices: GC content, nucleotide frequencies at codon position 3 (T3, C3, A3, G3), effective number of codons (ENc), GC3s, and relative synonymous codon usage (RSCU).
• Application of analytical methods: Parity rule 2 plot, Neutrality plot, ENc plot, and correlation analysis.
• Comparative analysis across 21 ciliate species with relatively complete genomes.

Main Results:

• The guanine-cytosine (GC) content in the MAC genomes of the studied ciliates was consistently below 50%.
• Distinct base compositions were observed for GC and GC3s across the species.
• Synonymous codon analysis indicated a prevalence of A- or T-ending codons, with four identified as putative optimal codons.

Conclusions:

• Most investigated ciliates exhibit a preference for AT-ending codons.
• Codon usage bias in these organisms is shaped by both gene mutation and natural selection.
• Understanding CUB is vital for advancing genetic research and gene editing applications in ciliates.