Development and characterization of 20 polymorphic microsatellite markers for Epinephelus marginatus (Lowe, 1834) (Perciformes: Epinephelidae) using 454 pyrosequencing

Abstract

The dusky grouper, Epinephelus marginatus, is a well-known and widespread marine fish assessed as endangered by the International Union for the Conservation of Nature. Analyzing the genetic diversity of this species is, therefore, of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informative. This suite of markers provides the first specific nuclear tools for E. marginatus and, thus, allows to assess with more specificity different populations’ structures.

Global population genetic structure of the sequential hermaphrodite, dusky grouper (Epinephelus marginatus)

“…Eleven highly polymorphic microsatellite loci (Ema01, Ema02, Ema04, Ema06, Ema17, Ema18, Ema20, Ema22, Ema23, Ema26, and Ema42) developed for dusky grouper (Vaini et al, 2019) were used to assess nuclear genetic variation among samples.…”

High genetic differentiation of Indo‐Pacific humpback dolphins (Sousa chinensis) along the Asian Coast of the Pacific Ocean

“…Traditional methods for microsatellite isolation include construction of an enriched library followed by cloning and Sanger sequencing, which are both expensive and extremely laborious and time‐consuming (Zane et al, 2002). With the development of next‐generation sequencing technologies, isolation of species‐specific microsatellite loci has become more convenient and efficient (Kumar & Kocour, 2017; Vaini et al, 2019). Paired‐end sequencing on the Illumina platform is currently the most commonly used approach for microsatellite isolation (González‐Castellano et al, 2018).…”

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

“…Molecular marker techniques are commonly used for fish stock characterization ( Cuéllar-Pinzón, et al, 2016 ). The identification, genetic diversity and estimate of genetic variation among grouper species have been reported by many scientists who used PCR based methods, including microsatellite ( Antoro et al, 2006 , Koedprang et al, 2007 , Wang et al, 2011 , Yang et al, 2011 , An et al, 2014 , Vaini et al, 2019 ), mitochondrial DNA ( Maggio et al, 2005 , Jackson et al, 2014 , Jefri et al, 2015 , Ketchum et al, 2016 , Galal-Khallaf et al, 2019 ), random amplified polymorphic DNA (RAPD) ( Govindaraju and Jayasankar, 2004 , Noikotr et al, 2013 , Roy et al, 2014 ) and inter simple sequence repeat (ISSR) ( Chiu, et al, 2012 ). Therefore, the current investigation aimed to determine genetic relationship and diversity among five Epinephelus spp.…”