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Lin P, Yu Y, Bao Z, Li F. Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in Litopenaeus vannamei. Int J Mol Sci 2024; 25:12083. [PMID: 39596153 PMCID: PMC11593832 DOI: 10.3390/ijms252212083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 11/28/2024] Open
Abstract
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 Litopenaeus vannamei (L. vannamei) 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.
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Affiliation(s)
- Pengfei Lin
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.L.); (Z.B.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.L.); (Z.B.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenning Bao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.L.); (Z.B.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.L.); (Z.B.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream ( Sparus aurata) Broodstock Nuclei. Genes (Basel) 2023; 14:839. [PMID: 37107597 PMCID: PMC10137967 DOI: 10.3390/genes14040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Fabrizio Capoccioni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Luca Buttazzoni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, 72016 Brindisi, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
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Signatures of Selection and Genomic Diversity of Muskellunge ( Esox masquinongy) from Two Populations in North America. Genes (Basel) 2021; 12:genes12071021. [PMID: 34209092 PMCID: PMC8303616 DOI: 10.3390/genes12071021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.
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Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Utzeri VJ, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. A comparative whole genome sequencing analysis identified a candidate locus for lack of operculum in cultivated gilthead seabream (Sparus aurata). Anim Genet 2021; 52:365-370. [PMID: 33609290 DOI: 10.1111/age.13049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2021] [Indexed: 01/29/2023]
Abstract
The gilthead seabream (Sparus aurata, Sparidae family) is commonly used for aquaculture. Despite its great economic value, several problems in its cultivation remain. One of the major concerns is the high frequency of morphological abnormalities occurring during the early developmental stages. Partial and/or total lack of operculum is the most frequent anomaly affecting the fish cranial region. The existence of genetic factors that can at least partially determine this defect has been hypothesized. In this work, two DNA pools of highly related fry, one composed of normal-looking (control) fish and the other lacking an operculum (case), were constructed and whole-genome resequencing data produced from the two were compared. The analysis revealed a 1 Mb region on chromosome 2 with higher heterozygosity in the lack of operculum DNA pool than in the control DNA pool, consistent with the enrichment, in the first DNA pool, of one or more haplotypes causing or predisposing to the defect together with other normal haplotypes. A window-based FST analysis between the two DNA pools indicated that the same region had the highest divergence score. This region contained 2921 SNVs, 10 of which, with predicted high impacts (three splice donor and seven stop-gained variants), were detected in novel genes that are homologous to calcium-sensing receptor-like genes, probably involved in bone development. Other studies are needed to clarify the genetic mechanisms involved in predisposing fry to this deformity and then to identify associated markers that could be used in breeding programs to reduce the frequency of this defect in the broodstock.
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Affiliation(s)
- F Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - F Capoccioni
- Centro di ricerca 'Zootecnia e Acquacoltura', Consiglio per la Ricerca in Agricoltura e L'Analisi dell'Economia Agraria, Via Salaria 31, Monterotondo, Roma, 00015, Italy
| | - L Buttazzoni
- Centro di ricerca 'Zootecnia e Acquacoltura', Consiglio per la Ricerca in Agricoltura e L'Analisi dell'Economia Agraria, Via Salaria 31, Monterotondo, Roma, 00015, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, Brindisi, 72016, Italy
| | - M F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
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