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

Author(s)

Raquel Siccha-Ramirez, Zoila ^{[1, 2]} ; Maroso, Francesco ^{[3, 4]} ; Pardo, Belen G. ^[3] ; Fernandez, Carlos ^[3] ; Martinez, Paulino ^[3] ; Oliveira, Claudio ^[1]

Affiliation

^[1] UNESP, Inst Biociencias, Dept Morfol, BR-18618970 Botucatu, SP - Brazil

^[2] Inst Mar Peru, Lab Costero Tumbes, Zorritos - Peru

^[3] Univ Santiago de Compostela, Fac Vet, Dept Zooloxia Xenet & Antropoloxia Fis, Campus Lugo, Lugo 27002 - Spain

^[4] Univ Padua, Dipartimento Biomed Comparata & Alimentaz BCA, Padua - Italy

• Document type: Journal article
• Source: Fisheries Research; v. 198, p. 189-194, FEB 2018.
• Web of Science Citations: 4

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 (Sbfl and Sphl) and fragments between 300 and 600 by 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 silica 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 (similar to 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. (AU)

• FAPESP's process: 11/00881-1 - Analysis of the composition and geographical distribution of tunas from the Brazilian coast (Perciformes: Scombridae: Thunnini)
• Grantee: Zoila Raquel Siccha Ramirez
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 13/07560-1 - Populational studies of yellowfin tuna (Thunnus albacares) and Serra Spanish mackerel (Scomberomorus brasiliensis) (Perciformes: Scombridae) using the reduced representation library technique
• Grantee: Claudio de Oliveira
• Support Opportunities: Regular Research Grants