Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cultures
2.2. Sequencing, Assembly, and Annotation
2.3. Phylogenetic Analysis
2.4. Substitution Rate Estimation
3. Results
3.1. Mitochondrial Genome of Colonial Volvocine Algae
3.2. Phylogenetic Analysis
3.3. Substitution Rate Estimation
4. Discussion
4.1. Phylogenetic Analysis
4.2. Substitution Rate Estimation
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Cell Number a | Size (kb) | GC Content | Number of Scaffold | Number of Genes | Genbank Accession | ||
---|---|---|---|---|---|---|---|---|
Protein-Coding Genes b | rRNA Genes | tRNA Genes | ||||||
Tetrabaena socialis | 4 | 28 | 45% | 1 | 9 | 12 | 3 | KX232644 |
Gonium pectorale | 8–32 | 16 | 39% | 1 | 8 | 12 | 4 | AP012493 |
Pandorina morum | 8–16 | 15 | 45% | 5 | 7 | 3 | 1 | MN431468-MN431472 |
Pandorina colemaniae | 8–16 | 19 | 38% | 1 | 8 | 9 | 3 | MN431473 |
Volvulina compacta | 8–16 | 22 | 41% | 1 | 8 | 6 | 4 | MN431476 |
Colemanosphaera angeleri | 16–32 | 18 | 38% | 1 | 10 | 8 | 3 | MN431475 |
Colemanosphaera charkowiensis | 16–32 | 24 | 38% | 1 | 9 | 8 | 3 | MN431474 |
Yamagishiella unicocca | 16–32 | 24 | 41% | 1 | 9 | 12 | 3 | MN431477 |
Yamagishiella unicocca | 16–32 | 31 | 41% | 1 | 12 | 12 | 3 | KY442293 |
Eudorina elegans | 16–32 | 27 | 33% | 1 | 11 | 12 | 3 | MH161346 |
Eudorina cylindrica | 16–32 | 26 | 36% | 1 | 9 | 12 | 3 | MH223465 |
Eudorina sp. | 16–32 | 21 | 38% | 1 | 9 | 12 | 3 | KY442294 |
Pleodorina starrii | 32–128 | 20 | 38% | 1 | 10 | 12 | 3 | JX977845 |
Volvox carteri | 500–50,000 | 35 | 34% | 1 | 10 | 13 | 3 | GU084821 |
Species | Synonymous Substitution (dS) | Nonsynonymous Substitution (dN) | dN/dS | ||||||
---|---|---|---|---|---|---|---|---|---|
mtDNA | ptDNA | mt:pt | mtDNA | ptDNA | mt:pt | mtDNA | ptDNA | mt:pt | |
Chlamydomonas reinhardtii | 2.2 ± 0.87 | 1.31 ± 0.83 | 1.8:1 | 0.05 ± 0.02 | 0.03 ± 0.03 | 2.17:1 | 0.03 ± 0.01 | 0.02 ± 0.02 | 1.36:1 |
Tetrabaena socialis | 2.57 ± 0.73 | 0.95 ± 0.52 | 2.74:1 | 0.05 ± 0.02 | 0.02 ± 0.03 | 2.33:1 | 0.02 ± 0.01 | 0.02 ± 0.03 | 0.88:1 |
Gonium pectorale | 2.41 ± 0.86 | 0.93 ± 0.51 | 2.84:1 | 0.05 ± 0.02 | 0.02 ± 0.02 | 2.67:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 1.12:1 |
Pandorina morum | 2.85 ± 0.66 | 0.82 ± 0.51 | 3.5:1 | 0.05 ± 0.02 | 0.02 ± 0.03 | 2.65:1 | 0.02 ± 0.01 | 0.02 ± 0.03 | 0.78:1 |
Pandorina colemaniae | 2.25 ± 0.76 | 1.14 ± 0.65 | 2.07:1 | 0.04 ± 0.02 | 0.02 ± 0.03 | 1.92:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 1.1:1 |
Volvulina compacta | 2.54 ± 0.92 | 1.13 ± 0.64 | 2.39:1 | 0.05 ± 0.02 | 0.03 ± 0.03 | 1.85:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 0.96:1 |
Colemanosphaera angeleri | 2.38 ± 1.13 | 1.24 ± 0.69 | 1.95:1 | 0.04 ± 0.02 | 0.03 ± 0.04 | 1.33:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 0.87:1 |
Colemanosphaera charkowiensis | 2.35 ± 1.11 | 0.82 ± 0.54 | 2.96:1 | 0.04 ± 0.02 | 0.02 ± 0.03 | 2.11:1 | 0.02 ± 0.01 | 0.02 ± 0.03 | 0.81:1 |
Yamagishiella unicocca | 1.97 ± 0.72 | 0.8 ± 0.52 | 2.55:1 | 0.04 ± 0.02 | 0.02 ± 0.02 | 2.03:1 | 0.02 ± 0.01 | 0.02 ± 0.03 | 0.81:1 |
Eudorina elegans | 2.57 ± 1.22 | 0.83 ± 0.61 | 3.1:1 | 0.04 ± 0.03 | 0.02 ± 0.02 | 2.62:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 0.93:1 |
Eudorina cylindrica | 2.49 ± 1.24 | 0.78 ± 0.55 | 3.37:1 | 0.05 ± 0.03 | 0.02 ± 0.02 | 2.64:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 0.86:1 |
Pleodorina starrii | 2.51 ± 1.25 | 0.81 ± 0.57 | 3:1 | 0.04 ± 0.03 | 0.02 ± 0.03 | 2.44:1 | 0.02 ± 0.01 | 0.02 ± 0.03 | 0.79:1 |
Volvox carteri | 2.42 ± 1.18 | 0.78 ± 0.56 | 3.21:1 | 0.05 ± 0.02 | 0.02 ± 0.02 | 2.58:1 | 0.02 ± 0.01 | 0.02 ± 0.02 | 0.91:1 |
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Hu, Y.; Xing, W.; Hu, Z.; Liu, G. Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes. Genes 2020, 11, 115. https://doi.org/10.3390/genes11010115
Hu Y, Xing W, Hu Z, Liu G. Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes. Genes. 2020; 11(1):115. https://doi.org/10.3390/genes11010115
Chicago/Turabian StyleHu, Yuxin, Weiyue Xing, Zhengyu Hu, and Guoxiang Liu. 2020. "Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes" Genes 11, no. 1: 115. https://doi.org/10.3390/genes11010115
APA StyleHu, Y., Xing, W., Hu, Z., & Liu, G. (2020). Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes. Genes, 11(1), 115. https://doi.org/10.3390/genes11010115