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| Auteurs principaux: | , , , |
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| Format: | Artículo científico |
| Langue: | en |
| Publié: |
International journal of molecular sciences
2024
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| Sujets: | |
| Accès en ligne: | https://pubmed.ncbi.nlm.nih.gov/39596153/ |
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| _version_ | 1868266275382231041 |
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| author | Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua |
| author_facet | Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua |
| collection | PubMed - marine biology |
| contents | Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in . Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua Polymorphism, Single Nucleotide Animals Penaeidae High-Throughput Nucleotide Sequencing Whole Genome Sequencing Genotyping Techniques Genotype Genome The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 () samples at over 28× sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5× to 20×. Results showed that when the sequencing depth was below 10×, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10× accounting for approximately 69.16% of those detected at 20×. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6×. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10× is recommended for whole-genome studies and genetic mapping, while a depth of 6× is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species. |
| format | Artículo científico |
| id | pubmed_39596153 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | International journal of molecular sciences |
| record_format | pubmed |
| spellingShingle | Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in . Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua Polymorphism, Single Nucleotide Animals Penaeidae High-Throughput Nucleotide Sequencing Whole Genome Sequencing Genotyping Techniques Genotype Genome Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in . Lin, Pengfei Yu, Yang Bao, Zhenning Li, Fuhua Polymorphism, Single Nucleotide Animals Penaeidae High-Throughput Nucleotide Sequencing Whole Genome Sequencing Genotyping Techniques Genotype Genome The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 () samples at over 28× sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5× to 20×. Results showed that when the sequencing depth was below 10×, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10× accounting for approximately 69.16% of those detected at 20×. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6×. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10× is recommended for whole-genome studies and genetic mapping, while a depth of 6× is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species. |
| title | Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in . |
| topic | Polymorphism, Single Nucleotide Animals Penaeidae High-Throughput Nucleotide Sequencing Whole Genome Sequencing Genotyping Techniques Genotype Genome |
| url | https://pubmed.ncbi.nlm.nih.gov/39596153/ |