SNP identification and validation on genomic DNA for studying genetic diversity in Thunnus albacares and Scomberomorus brasiliensis by combining RADseq and long read high throughput sequencing

Abstract

A combination of a RADseq method (ddRAD) with long read high throughput sequencing (Roche 454) was tuned up in order to identify and validate a set of SNPs useful for gene diversity analysis in two important South American commercial tuna (Thunnus albacares and Scomberomorus brasiliensis). A total of 11 and 21 individuals of T. albacares and S. brasiliensis, respectively, were used for SNP identification. DNA was individually digested with two restriction enzymes (SbfI and SphI) and fragments between 300 and 600 bp selected. Combinatorial barcoding was used to identify individuals by including short sequences (5-7 bp) in the adaptors of each restriction site (P1 and P2). After adaptor ligation, samples were pooled and size-selected, amplified by PCR, and sequenced on a 454 GS-Junior sequencer. A total of 180,779 reads were produced with an average length and coverage of 287 bp and 26x, respectively. Sets of 60 and 79 SNPs were in silico selected for T. albacares and S. brasiliensis, respectively, and were tested and validated in 74 and 66 individuals, respectively, on a MassARRAY platform. A total of 36 and 47 SNPs were polymorphic and useful for population analysis. A preliminary study on two distant Brazilian populations of both species (∼3000 km) with these SNPs suggested the absence of significant structure among local populations of both species. Our results demonstrate the possibility of combining ddRAD with long read high throughput sequencing for marker development in species with scarce genomic resources.

Molecular Inferences on Scomberomorus brasiliensis, From the Western South Atlantic, Based on Two Mitochondrial Genes

“…A similar pattern of genetic connectivity has been observed in other fish species, such as the King mackerel, Scomberomorus cavalla, on the northern and northeastern coasts of Brazil (Santa Brígida et al, 2007), and the red snapper, Lutjanus campechanus, and Acoupa weakfish, Cynoscion acoupa, populations of the Brazilian coast, in which no structuring was found in mitochondrial markers (Broughton et al, 2002;Gomes et al, 2008;Rodrigues et al, 2008;Silva et al, 2015). Furthermore, Siccha-Ramírez et al (2018) utilizing SNPs (Single Nucleotide Polymorphisms) analyze samples from two commercially important species (S. brasiliensis and Thunnus albacares), where the results suggest the absence of any genetic structure among the local populations for both species, despite the sampling points are distant approximately 3,000 km.…”

“…The genetic variability observed in the S. brasiliensis population sampled in the present study is important for the definition of effective conservation strategies, with the primary objective of mediating the decline of the population and guaranteeing the sustainability of this fishery resource (Ward, 2000;López et al, 2010;Souza-Shibatta et al, 2018;Córdova-Alarcón et al, 2019). Given this, further research on the S. brasiliensis populations should adopt a multi-locus approach integrating microsatellites, SNPs, and RADseq (see Siccha-Ramírez et al, 2018), which would complement the findings of the present study, based on two mtDNA loci. The findings of the present study provide important insights into the genetic diversity and the potential distribution of the stocks of S. brasiliensis and provide a fundamental contribution to the development of effective, longterm management strategies for the populations of the species.…”

Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing

“…Both RAD and ddRAD-seq have been widely applied in aquaculture breeding and genetics studies (Robledo et al 2018). In particular, ddRAD-seq has been applied for genotyping large multiplexed datasets (e.g., Maroso et al 2018), construction of genetic linkage maps (e.g., Recknagel et al 2013;Oral et al 2017), analyzing life history traits (e.g., Pukk 2016), mapping sex determining loci (e.g., Palaiokostas et al 2015;Brown et al 2016), genomic predictions and genome-wide association studies (e.g., Barria et al 2018), assessing genetic diversity (e.g., Hosoya et al 2018;Tony et al 2015;Siccha-Ramirez et al 2018;Torati et al 2019), phylogeography (e.g., Stobie et al 2018, and species identification in tilapias (Syaifudin et al 2019).…”

Barriers to gene flow along the Brazilian coast: a synthesis and data analysis

“…Microsatellites remain a poorly used technique with only 29 studies (12%) published since 2001 (Beheregaray & Sunnucks, 2001). A similar pattern was observed for genome-wide techniques, such as SNPs, where only one marine study was published to date (Siccha-Ramirez et al, 2018). In the world, genome wide SNP and high-throughput DNA sequencing techniques are becoming the powerhouse in phylogeographic studies (e.g.…”

“…Only four articles (6%) targeted autotrophic organisms, two terrestrial vascular plants (mangroves) and two red macroalgae, and two of them used chloroplast-encoded markers (Ayres-Ostrock et al, 2019;Mori, Zucchi, Sampaio, & Souza, 2015). Only one more recent article used the SNP technique (Siccha-Ramirez et al, 2018).…”