Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction and Library Preparation
2.3. Sequence Assembly, Filtering and SNPs Discovery
2.4. Power Analysis
2.5. Genetic Variation Analysis
2.6. GO and KEGG Enrichment Analysis of Putatively Adaptive SNP Loci
2.7. Data Accessibility
3. Results
3.1. Genome Assembly, Annotation and Quality Filtering of SNP Loci
3.2. Power Analysis
3.3. Demographic Interpretations from FST Statistics and AMOVA Analysis
3.4. Genetic Structure Based on Clustering Analyses
3.5. GO Categorization of the Encoding Genes of Putatively Adaptive SNP Loci
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Locations | Location Abbreviation | Broodstock Source | Latitudes | Longitudes | Year |
---|---|---|---|---|---|
Mahajamba, Madagascar | MMD | Domesticated | 16°02′52.8″ | 47°11′38.0″ | 2018 |
Hawaii, HI, USA | MMO | Domesticated | 19°42′55.9″ | 156°02′34.6″ | 2018 |
Petchaburi Province, Thailand | MT | Domesticated | 12°58′06.5″ | 99°37′48.0″ | 2019 |
Setiu Wetland, Malaysia | MS | Wild | 5°40′38.3″ | 102°42′36.8″ | 2019 |
Shizuoka, Japan | MJ | Wild | 34°56′25.9″ | 138°02′17.9″ | 2018 |
Genome Assembly Statistics | |
Number of scaffolds | 6,425,442 |
Size of largest scaffolds (bp) | 15,300 |
Size of smallest scaffolds (bp) | 100 |
Total scaffold size (bp) | 1,531,786,734 |
Scaffold N50 | 306 |
Genome annotation statistics | |
Number of Scaffolds with at least one protein sequence match | 440,707 |
Number of Decapoda (order) protein sequences with match to scaffold | 107,063 |
Number of SwissProt protein sequences with match to scaffold | 42,351 |
Variant identification results | |
Number of Scaffolds with at least one variant site | 3,651,235 |
Total number of variants | 17,226,908 |
Variant annotation results | |
Total number of variants with annotations | 1,347,070 |
Number of variants annotated with Decapoda proteins | 1,339,785 |
Number of variants annotated with SwissProt proteins | 142,710 |
Filtering Steps | Number of Loci |
---|---|
Total number of raw variants loci | 17,226,908 |
Remaining SNP loci after excluded indels and MNP sites | 13,530,393 |
Remaining SNP loci after excluded sites with MAF < 0.05 | 10,212,187 |
Remaining SNP loci after excluded sites with missing genotypes in >80% of the samples in any population | 417,048 |
Remaining SNP loci after excluded sites with genotypes not in Hardy-Weinberg equilibrium in any population (PHWE < 0.001) | 328,028 |
SNP loci remained after all quality filtering | 194,259 |
Number of putatively adaptive SNP loci | 4983 |
All 194,259 SNP Loci | 4983 Putatively Adaptive SNP Loci | ||||
---|---|---|---|---|---|
t | Ne | Power | t | Ne | Power |
10 | 1000 | 0.945 | 10 | 1000 | 1.000 |
20 | 1000 | 1.000 | 20 | 1000 | 1.000 |
10 | 2000 | 0.884 | 10 | 2000 | 1.000 |
20 | 2000 | 0.912 | 20 | 2000 | 0.994 |
10 | 3000 | 0.824 | 10 | 3000 | 0.996 |
20 | 3000 | 0.902 | 20 | 3000 | 0.985 |
Wild | Domesticated | ||||
---|---|---|---|---|---|
MJ | MS | MMO | MMD | MT | |
All SNP loci | |||||
MJ | -- | 0.001 | 0.001 | 0.001 | 0.001 |
MS | 0.008 | -- | 0.001 | 0.001 | 0.001 |
MMO | 0.151 | 0.147 | -- | 0.023 | 0.001 |
MMD | 0.150 | 0.145 | 0.003 | -- | 0.001 |
MT | 0.153 | 0.148 | 0.010 | 0.008 | -- |
Putatively adaptive SNP loci | |||||
MJ | -- | 0.000 | 0.000 | 0.000 | 0.000 |
MS | 0.106 | -- | 0.000 | 0.000 | 0.000 |
MMO | 0.836 | 0.856 | -- | 0.105 | 0.002 |
MMD | 0.853 | 0.870 | 0.003 | -- | 0.000 |
MT | 0.850 | 0.868 | 0.035 | 0.042 | -- |
Source of Variation | Sum of Square | Variance Components | % of Variation | Statistics | p-Value |
---|---|---|---|---|---|
All SNP loci | |||||
Within individuals | 1,056,256 | 25,309.931 | 74.1 | F_it = 0.259 | - |
Among individuals | 1,286,226.1 | 5502.952 | 16.1 | F_is = 0.179 | 0.000 |
Among populations | 355,088.8 | 3342.094 | 9.8 | F_st = 0.098 | 0.000 |
Putatively adaptive SNP loci | |||||
Within individuals | 10,205.5 | 238.184 | 19.2 | F_it = 0.808 | - |
Among individuals | 8192.9 | −0.083 | 0.0 | F_is = 0.000 | 0.483 |
Among populations | 63029.16 | 1004.217 | 80.8 | F_st = 0.808 | 0.000 |
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Wong, L.L.; Deris, Z.M.; Igarashi, Y.; Huang, S.; Asakawa, S.; Ayub, Q.; Lim, S.Y.; Ikhwanuddin, M.; Iehata, S.; Okamoto, K.; et al. Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region. Biology 2020, 9, 277. https://doi.org/10.3390/biology9090277
Wong LL, Deris ZM, Igarashi Y, Huang S, Asakawa S, Ayub Q, Lim SY, Ikhwanuddin M, Iehata S, Okamoto K, et al. Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region. Biology. 2020; 9(9):277. https://doi.org/10.3390/biology9090277
Chicago/Turabian StyleWong, Li Lian, Zulaikha Mat Deris, Yoji Igarashi, Songqian Huang, Shuichi Asakawa, Qasim Ayub, Shu Yong Lim, Mhd Ikhwanuddin, Shumpei Iehata, Kazutoshi Okamoto, and et al. 2020. "Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region" Biology 9, no. 9: 277. https://doi.org/10.3390/biology9090277