Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction, RAD-Seq Libraries Construction and Sequencing
2.3. Data Analysis
2.3.1. Data Processing, Assembly and Alignment
2.3.2. Genome-Wide Genetic Variation and Population Genetic Structure
2.3.3. Detection of Selection Footprints
3. Results
3.1. Data Processing, Assembly and Alignment
3.2. Genome-Wide Genetic Variation and Population Genetic Structure
3.3. Detection and Annotation of SNPs under Selection
4. Discussion
4.1. Genome-Wide Genetic Variation and Population Genetic Structure
4.2. Detection and Annotation of SNPs under Selection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Host Plant | Locality | Code | Number of Individuals |
---|---|---|---|
Averrhoa carambola | North | CaN | 26 |
South | CaS | 40 | |
Mangifera indica | North | MN | 40 |
South | MS | 40 | |
Spondias purpurea | North | RmN | 40 |
South | RmS | 40 |
Population | Accessions Code | Number of Raw Reads | Number of Aligned Reads | Number of SNPs | π | θW |
---|---|---|---|---|---|---|
CaN | SRR13442704 | 43,020,774 | 20,493,546 | 488,027 | 0.0105 a | 0.0112 b |
CaS | SRR13442703 | 43,183,116 | 21,589,043 | 565,527 | 0.0108 b | 0.0117 c |
RmN | SRR13442702 | 43,003,430 | 20,134,297 | 481,206 | 0.0106 a | 0.0115 a |
RmS | SRR13442701 | 43,036,924 | 20,554,814 | 503,735 | 0.0105 a | 0.0115 a |
MN | SRR13442700 | 43,020,380 | 20,765,409 | 524,277 | 0.0105 a | 0.0115 a |
MS | SRR13442699 | 43,048,340 | 21,039,009 | 546,956 | 0.0106 a | 0.0115 a |
Population | CaN | CaS | RmN | RmS | MN | MS |
---|---|---|---|---|---|---|
CaN | - | (0.0159–0.0166) | (0.0158–0.0164) | (0.0155–0.0161) | (0.0154–0.0160) | (0.0153–0.0159) |
CaS | 0.0162 | - | (0.0106–0.0111) | (0.0105–0.0110) | (0.0109–0.0116 | (0.0103–0.0108) |
RmN | 0.0161 | 0.0109 | - | (0.0117–0.0123) | (0.0112–0.0118) | (0.0108–0.0113) |
RmS | 0.0158 | 0.0107 | 0.0120 | - | (0.0109–0.0115) | (0.0107–0.0112) |
MN | 0.0157 | 0.0113 | 0.0115 | 0.0112 | - | (0.0112–0.0118) |
MS | 0.0156 | 0.0105 | 0.0111 | 0.0110 | 0.0115 | - |
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Aguirre-Ramirez, E.; Velasco-Cuervo, S.; Toro-Perea, N. Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature. Insects 2021, 12, 1116. https://0-doi-org.brum.beds.ac.uk/10.3390/insects12121116
Aguirre-Ramirez E, Velasco-Cuervo S, Toro-Perea N. Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature. Insects. 2021; 12(12):1116. https://0-doi-org.brum.beds.ac.uk/10.3390/insects12121116
Chicago/Turabian StyleAguirre-Ramirez, Elkin, Sandra Velasco-Cuervo, and Nelson Toro-Perea. 2021. "Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature" Insects 12, no. 12: 1116. https://0-doi-org.brum.beds.ac.uk/10.3390/insects12121116