Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species
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Título: | Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species
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Autor/a: | Casanova Chiclana, Adrián
Maroso, Francesco
Blanco Hortas, Andrés
Hermida Prieto, Miguel
Ríos, Néstor
García, Graciela
Manuzzi, Alice
Zane, Lorenzo
Veríssimo, Ana
García Marín, José Luis
Bouza Fernández, María Carmen
Vera Rodríguez, Manuel
Martínez Portela, Paulino
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Centro/Departamento: | Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física Universidade de Santiago de Compostela. Instituto de Acuicultura
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Palabras chave: | STACKS 2 | 2b-RAD v2.1 pipeline | de novo approach | Bowtie 1 | Reference genome approach | Bivalves | Fish | Population genomics | |
Data: | 2021
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Editor: | BMC
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Cita bibliográfica: | Casanova, A., Maroso, F., Blanco, A. et al. Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species. BMC Genomics 22, 150 (2021). https://doi.org/10.1186/s12864-021-07465-w
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Resumo: | 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 |
Versión do editor: | https://doi.org/10.1186/s12864-021-07465-w |
URI: | http://hdl.handle.net/10347/26137
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DOI: | 10.1186/s12864-021-07465-w |
ISSN: | 1471-2164
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Dereitos: | © The Author(s). 2021. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data Atribución 4.0 Internacional
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