Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Assembly of the Chlorovirus Dataset
2.2. Determination of Single-Copy Core Gene Pair Distances
2.2.1. Strictly Constrained Bin Analysis
2.2.2. Growing Bin Analysis
2.3. Determination of Phylogenetic Distances
2.4. Identification of Gene Gangs
2.5. Functional Annotation Methods
3. Results
3.1. Chlorovirus Genomic Stability
3.2. Conservation of Distance between Single Copy Core Genes
3.2.1. Results of Strictly Constrained Bin Analysis
3.2.2. Results of Growing Bin Analysis or Pairwise Distances
3.3. Identification of Gene Gangs
3.4. Topological Features of Selected Gene Gangs
3.5. Functional Evaluation of Gene Gangs
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Genes of Interest | Ruliness | ||||||
---|---|---|---|---|---|---|---|
0.826 | 0.854 | 0.902 | 0.927 | 0.951 | 0.976 | 1.00 | |
Core Genes | 66.9% | 65.5% | 63.5% | 60.4% | 60.4% | 57.7% | 53.1% |
All Genes | 35.2% | 33.7% | 31.5% | 29.3% | 29.0% | 27.7% | 24.8% |
Gang | Maximum Number of Gang Members | Consensus Number of Gene Members of the Gang in Block Diagram $ | Number of Viruses That Are Ruly (100% Conserved in Gene Content), Total = 41 | Number of Viruses That Maintain Synteny, Total = 41 | Number of Viruses with Strand Conservation, Total = 41 | Number of Viruses with Infiltrated Non-Gang (Alien) Genes, Total = 41 |
---|---|---|---|---|---|---|
1 | 11 | 10 | 38 | 41 | 39 | 41 |
2 | 9 | 8 | 40 | 40 | 40 | 41 |
3 | 9 | 9 | 41 | 41 | 27 | 38 |
4 | 8 | 8 | 38 | 27 | 27 & | 17 |
5 * | 7 | 6 | 37 | Virus type-specific | Virus type-specific | 23 |
6 | 6 | 6 | 34 | 40 | 40 | 41 |
7 | 7 | 7 | 40 | 28 | 28 | 21 |
8 | 6 | 6 | 35 | 27 | 27 | 25 |
9 | 6 | 5 | 39 | 39 | 28 | 37 |
10 | 5 | 5 | 33 | 33 | 33 | 3 |
11 | 5 | 5 | 34 | 34 | 34 | 41 |
12 | 5 | 4 | 40 | 40 | 40 | 35 |
13 | 4 | 4 | 40 | 40 | 27 | 13 |
14 | 4 | 4 | 35 | 35 | 35 | 38 |
15 | 4 | 4 | 34 | 27 | 27 | 30 |
16 | 4 | 4 | 35 | 35 | 35 | 26 |
17 | 4 | 4 | 41 | 27 | 27 | 35 |
18 | 4 | 4 | 41 | 41 # | 28 | 28 |
19 | 3 | 3 | 41 | 41 | 41 | 24 |
20 | 3 | 3 | 39 | 39 | 39 | 9 |
21 | 3 | 3 | 41 | 41 | 41 | 16 |
22 | 3 | 3 | 39 | 39 | 39 | 11 |
23 | 3 | 3 | 29 | 29 | 29 | 37 |
24 | 3 | 3 | 34 | 34 | 34 | 37 |
25 | 3 | 3 | 36 | 36 | 36 | 26 |
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Seitzer, P.; Jeanniard, A.; Ma, F.; Van Etten, J.L.; Facciotti, M.T.; Dunigan, D.D. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. Viruses 2018, 10, 576. https://doi.org/10.3390/v10100576
Seitzer P, Jeanniard A, Ma F, Van Etten JL, Facciotti MT, Dunigan DD. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. Viruses. 2018; 10(10):576. https://doi.org/10.3390/v10100576
Chicago/Turabian StyleSeitzer, Phillip, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, and David D. Dunigan. 2018. "Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes" Viruses 10, no. 10: 576. https://doi.org/10.3390/v10100576