Development and characterization of eighty-four microsatellite markers for the red snapper (Lutjanus campechanus) using Illumina paired-end sequencing

•Microsatellite loci were discovered by direct screening of Illumina sequences.•The red snapper is an important reef fish candidate for marine aquaculture.•New microsatellites are needed for on-going genomic and mapping studies.•The method will be useful for developing microsatellites de novo in other species.•The study provides empirical information on implementation of the method.

Eighty-four microsatellite loci were isolated from red snapper, Lutjanus campechanus, using Illumina paired-end sequencing and a direct ‘Seq-to SSR’ approach. The number of alleles per locus ranged from 7 to 30 and estimates of expected heterozygosity ranged from 0.466 to 0.967 (n = 30). Genotype frequencies at 7 loci deviated significantly from Hardy-Weinberg expectations; the departure at 4 of these loci likely reflects the segregation of null alleles. The markers characterized in this work will be applied to linkage mapping and genetic studies involved in the domestication and stock enhancement of red snapper. Development of the 84 microsatellites required screening approximately 1.5 M paired-end reads, highlighting the potential of this method for rapid and cost-effective development of new homologous microsatellites in emerging aquaculture species.