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| Main Authors: | , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
International journal of molecular sciences
2025
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/40429742/ |
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| _version_ | 1868266198729228288 |
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| author | Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun |
| author_facet | Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun |
| collection | PubMed - marine biology |
| contents | Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone . Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun Animals Polymorphism, Single Nucleotide Gastropoda Whole Genome Sequencing Genotype Gene Frequency Genome High-Throughput Nucleotide Sequencing Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of low-coverage whole-genome sequencing (lcWGS) combined with imputation for genotyping in Pacific abalone () without a reference panel. We utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86×, as well as 16 individuals sequenced at 20×, as sample materials. To assess the genotype imputation accuracy for lcWGS without a reference panel, we simulated data with varying sequencing depths (0.5-4×) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF) using BaseVar and STITCH strategies. Results showed that STITCH achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R) of 0.98 ± 0.002 and genotype concordance (GC) of 0.99 ± 0.001. Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1×. Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98. However, the accuracy for rare MAF ( |
| format | Artículo científico |
| id | pubmed_40429742 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | International journal of molecular sciences |
| record_format | pubmed |
| spellingShingle | Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone . Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun Animals Polymorphism, Single Nucleotide Gastropoda Whole Genome Sequencing Genotype Gene Frequency Genome High-Throughput Nucleotide Sequencing Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone . Fei, Chengxia Zhang, Shoudu Chen, Xiangrui Liu, Junyu Peng, Wenzhu Zhang, Guofan You, Weiwei Wu, Fucun Animals Polymorphism, Single Nucleotide Gastropoda Whole Genome Sequencing Genotype Gene Frequency Genome High-Throughput Nucleotide Sequencing Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of low-coverage whole-genome sequencing (lcWGS) combined with imputation for genotyping in Pacific abalone () without a reference panel. We utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86×, as well as 16 individuals sequenced at 20×, as sample materials. To assess the genotype imputation accuracy for lcWGS without a reference panel, we simulated data with varying sequencing depths (0.5-4×) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF) using BaseVar and STITCH strategies. Results showed that STITCH achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R) of 0.98 ± 0.002 and genotype concordance (GC) of 0.99 ± 0.001. Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1×. Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98. However, the accuracy for rare MAF ( |
| title | Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone . |
| topic | Animals Polymorphism, Single Nucleotide Gastropoda Whole Genome Sequencing Genotype Gene Frequency Genome High-Throughput Nucleotide Sequencing |
| url | https://pubmed.ncbi.nlm.nih.gov/40429742/ |