Casanova Adrián, Maroso Francesco, Blanco Andrés, Hermida Miguel, Ríos Néstor, García Graciela, Manuzzi Alice, Zane Lorenzo, Verissimo Ana, García-Marín José-Luís, Bouza Carmen, Vera Manuel, Martínez Paulino
Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002, Lugo, Spain.
Present address: Dipartimento di Scienze della Vita e Biotecnologia (SVeB), Università degli Studi di Ferrara, via Luigi Borsari, 46 - 44121, Ferrara, Italy.
BMC Genomics. 2021 Mar 2;22(1):150. doi: 10.1186/s12864-021-07465-w.
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.
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.
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.
过去十年中，新一代测序（NGS）和限制性位点相关DNA测序（RAD-seq）的出现使得数千种分子标记得以鉴定，并对其进行基因分型以实现精细的基因组筛选。这种方法对于基因组资源有限的非模式生物尤为有用。已经开发了许多构建位点流程，以使用从头RAD-seq方法（即无需参考基因组）获得可靠的单核苷酸多态性（SNP）基因分型数据集。在此，使用代表不同基因组和/或种群结构情景的多种水生物种，比较了两种构建位点流程STACKS 2和迈耶的2b-RAD v2.1流程的性能。研究了两种双壳类物种（菲律宾蛤仔和食用蚶）和三种鱼类（褐鳟、银鲶和猫鲨）。在每个物种中评估了四个SNP面板，以测试不同的构建位点流程和SNP选择标准。此外，对于菲律宾蛤仔和褐鳟，使用参考基因组方法作为对照。
尽管在所测试的不同SNP调用和过滤步骤中，流程和物种之间观察到了不同的结果，但使用从头方法获得的SNP面板在物种内的遗传多样性和分化方面未发现显著差异。在褐鳟中，从头方法和参考基因组方法之间发现了主要差异。在两个构建位点流程之间或从头方法与参考基因组比较之间检测到的主要基因分型差异是基因分型数据与缺失数据的不匹配。
用于选择SNP面板的经过测试的构建位点流程似乎对本研究中各种案例研究情景下的群体遗传学推断影响较小。然而，建议根据每项研究的具体目标，对不同的生物信息学流程进行初步试验，以评估它们对群体参数的影响。
