Codon Usage Bias in Phytoplankton
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Preparation
2.2. Codon Bias Analysis
2.3. The Analysis of Genetic Diversity within Species
3. Results
3.1. Codon Bias Analysis
3.2. GC Content and Optimal Codon Shift
3.3. Sequence Diversity within Species
4. Discussion
4.1. Patterns of CUB in Phytoplankton
4.2. The Prevalence of GC-Rich Optimal Codons
4.3. Shifts between GC- and AT-Ending Preferred Codons
4.4. Mutation Bias
4.5. Low CUB and Genetic Diversity in Marine Phytoplankton
4.6. Do the Peculiarities of the Genome or Cell Structure Affect CUB?
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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GC3 (%) | Average | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Group | Nstrains | Nspecies | <25 | 25–35 | >35–45 | >45–55 | >55–65 | >65–75 | >75 | GC3 | GC | FOP | ENC |
Haptophyta | 24 | 19 | 0 | 0 | 0 | 0 | 3 | 10 | 11 | 72.9 | 64.7 | 0.49 | 45.9 |
Cryptophyta | 19 | 16 | 0 | 0 | 0 | 0 | 8 | 10 | 1 | 66.7 | 58.2 | 0.45 | 51.6 |
Dinophyta | 44 | 41 | 0 | 0 | 0 | 4 | 15 | 17 | 8 | 65.8 | 59.6 | 0.46 | 51.5 |
Chlorophyta | 49 | 38 | 0 | 0 | 1 | 6 | 9 | 18 | 15 | 68.9 | 61.1 | 0.48 | 47.9 |
Unicellular Rhodophyta | 8 | 8 | 0 | 0 | 1 | 3 | 3 | 1 | 0 | 55.4 | 54.1 | 0.45 | 54.2 |
Chlorarachniophyta | 12 | 9 | 0 | 1 | 0 | 6 | 5 | 0 | 0 | 53.4 | 50.9 | 0.43 | 58.0 |
Ciliophora | 19 | 19 | 0 | 1 | 6 | 4 | 6 | 2 | 0 | 51.0 | 48.7 | 0.44 | 52.9 |
Ochrophyta | 40 | 34 | 3 | 4 | 3 | 3 | 10 | 13 | 4 | 56.6 | 54.3 | 0.44 | 50.2 |
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Krasovec, M.; Filatov, D.A. Codon Usage Bias in Phytoplankton. J. Mar. Sci. Eng. 2022, 10, 168. https://doi.org/10.3390/jmse10020168
Krasovec M, Filatov DA. Codon Usage Bias in Phytoplankton. Journal of Marine Science and Engineering. 2022; 10(2):168. https://doi.org/10.3390/jmse10020168
Chicago/Turabian StyleKrasovec, Marc, and Dmitry A. Filatov. 2022. "Codon Usage Bias in Phytoplankton" Journal of Marine Science and Engineering 10, no. 2: 168. https://doi.org/10.3390/jmse10020168
APA StyleKrasovec, M., & Filatov, D. A. (2022). Codon Usage Bias in Phytoplankton. Journal of Marine Science and Engineering, 10(2), 168. https://doi.org/10.3390/jmse10020168