Gene Conversion Explains Elevated Diversity in the Immunity Modulating APL1 Gene of the Malaria Vector Anopheles funestus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identifying APL, LRIM, TEP and AMP Genes in An. funestus
2.2. Variant Prediction from Genome-Wide Pooled-Sequencing
2.3. Targeted Sequencing of Candidate Resistance Genes and Regions
2.4. Fst-Based Associations between Resistant and Susceptible Mosquitoes within Each Country
2.5. Gene Expression of APL1, TEP and LRIM Genes
2.6. Identifying Shared Polymorphisms and Recombination between APL1 Paralogues
3. Results
3.1. Immune Gene Complements of An. funestus
3.2. APL1 Has Elevated Diversity
3.3. Haplotype Analyses and Fst between Countries Reveals No Clustering by Resistance or Origin
3.4. Gambicin and Other Immune-Related Genes Are Also Highly Polymorphic
3.5. APL1 Expression Is Greater Than Its Paralogues and a Subset of AMPs Are Very Highly Expressed
3.6. Discordant Read Mappings Consistent with Gene Conversion between APL1 Paralogues
4. Discussion
4.1. Gene Conversion Explains Elevated APL1 Diversity in An. funestus
4.2. Gene Conversion Acts on APL1 Orthologues in Other Anopheles Species
4.3. Elevated πN in the An. funestus Anti-Microbial Protein Gambicin
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene | Nonsynonymous Sites | Synonymous Sites | πN | πS |
---|---|---|---|---|
PoolSeq | ||||
APL1/AFUN018743 | 1475.80 | 426.20 | 0.027 | 0.036 |
AFUN018581 | 1396.35 | 409.62 | 0.023 | 0.036 |
AFUN000279 | 1399.86 | 406.14 | 0.010 | 0.012 |
AFUN000288 | 2320.70 | 688.30 | 0.012 | 0.019 |
AFUN000597 | 1401.36 | 404.64 | 0.008 | 0.008 |
SureSelect | ||||
APL1/AFUN018743 | 1461.21 | 418.62 | 0.025 | 0.027 |
AFUN018581 | 1389.97 | 402.91 | 0.019 | 0.023 |
AFUN000279 | 1389.10 | 402.13 | 0.022 | 0.028 |
AFUN000288 | 2313.82 | 689.23 | 0.017 | 0.025 |
AFUN000597 | 1398.40 | 404.38 | 0.018 | 0.020 |
Gene | Original Coverage | Discordant Read Filtered Coverage |
---|---|---|
AFUN018743 | 48.31 | 42.79 |
AFUN018581 | 49.55 | 43.16 |
AFUN000279 | 20.79 | 17.06 |
AFUN000288 | 23.12 | 20.48 |
AFUN000597 | 14.60 | 12.15 |
All genes | 33.98 | N/A |
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Hearn, J.; Riveron, J.M.; Irving, H.; Weedall, G.D.; Wondji, C.S. Gene Conversion Explains Elevated Diversity in the Immunity Modulating APL1 Gene of the Malaria Vector Anopheles funestus. Genes 2022, 13, 1102. https://doi.org/10.3390/genes13061102
Hearn J, Riveron JM, Irving H, Weedall GD, Wondji CS. Gene Conversion Explains Elevated Diversity in the Immunity Modulating APL1 Gene of the Malaria Vector Anopheles funestus. Genes. 2022; 13(6):1102. https://doi.org/10.3390/genes13061102
Chicago/Turabian StyleHearn, Jack, Jacob M. Riveron, Helen Irving, Gareth D. Weedall, and Charles S. Wondji. 2022. "Gene Conversion Explains Elevated Diversity in the Immunity Modulating APL1 Gene of the Malaria Vector Anopheles funestus" Genes 13, no. 6: 1102. https://doi.org/10.3390/genes13061102
APA StyleHearn, J., Riveron, J. M., Irving, H., Weedall, G. D., & Wondji, C. S. (2022). Gene Conversion Explains Elevated Diversity in the Immunity Modulating APL1 Gene of the Malaria Vector Anopheles funestus. Genes, 13(6), 1102. https://doi.org/10.3390/genes13061102