Adrián Casanova1, Francesco Maroso1,2, Andrés Blanco1, Miguel Hermida1, Néstor Ríos3, Graciela García3, Alice Manuzzi4, Lorenzo Zane5,6, Ana Verissimo7,8, José-Luís García-Marín9, Carmen Bouza1,10, Manuel Vera11,12, Paulino Martínez1,10. 1. Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain. 2. Present address: Dipartimento di Scienze della Vita e Biotecnologia (SVeB), Università degli Studi di Ferrara, via Luigi Borsari, 46 - 44121, Ferrara, Italy. 3. Sección Genética Evolutiva. Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay. 4. National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark. 5. Department of Biology, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy. 6. Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy. 7. CIBIO - U.P. - Research Center for Biodiversity and Genetic Resources, Campus Agrário de Vairão, 4485-661, Vairão, Portugal. 8. Virginia Institute of Marine Science, College of William and Mary, Route 1208, Greate Road, Gloucester Point, VA, 23062, USA. 9. Laboratori d'Ictiologia Genètica, Departamento de Biología, Faculty of Sciences, University of Girona, Campus of Montilivi, ES-17071, Girona, Spain. 10. Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain. 11. Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain. manuel.vera@usc.es. 12. Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain. manuel.vera@usc.es.
Abstract
BACKGROUND: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer's 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. RESULTS: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. CONCLUSIONS: Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.
BACKGROUND: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer's 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. RESULTS: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. CONCLUSIONS: Tested building-loci pipelines for selection of SNP panels seem to have low influence on population genetics inference across the diverse case-study scenarios here studied. However, preliminary trials with different bioinformatic pipelines are suggested to evaluate their influence on population parameters according with the specific goals of each study.
Entities:
Keywords:
2b-RAD v2.1 pipeline; Bivalves; Bowtie 1; Fish; Population genomics; Reference genome approach; STACKS 2; de novo approach
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