Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)

Abstract

Objectives: Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. Methods: The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. Results: A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. Conclusions: The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes ( FIS = 0.155) in one breeding population provide baseline information for future breeding program.

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta)

“…The choice of simple sequence repeats (SSRs) as genetic markers in this genome survey was made after a review of the relevant literature. SSRs have been used as genetic tools in fish and aquaculture for linkage map construction [ 30 ], assessment of genetic diversity [ 31 ], parentage determination [ 32 ], and a genome-wide association study [ 33 ]. The information on SSRs in R. brachysoma and R. kanagurta could be benefit further studies of genetic markers in mackerels.…”

Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

“…In this study, a total of 412,381 SSRs were identified and accounted for 1.24% of the reference genome length. The genome-wide SSR content was similar to that of Takifugu rubripes (0.77%), Takifugu flavidus (0.73%) [ 28 ], and Monopterus albus (1.03%) [ 29 ]. Among different types of repeats, A/T motifs were considerably more common than G/C motifs (see Figure 2 ).…”

Microsatellite Characteristics of Silver Carp (Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations

“…The frequency of SSRs in H. molitrix was 437.73 loci/Mb, lower than that in Cyprinus carpio (621.95 loci/Mb), Oncorhynchus kisutch (461.35 loci/Mb), and Cynoglossus semilaevis (3445.94 loci/Mb) [ 30 ], and higher than that in some birds (80.9–256.9 loci/Mb) [ 26 ] and Lateolabrax maculatus (425.06 loci/Mb) [ 31 ]. The density (7713.16 bp/Mb) was higher than that of Ctenopharyngodon idella (1425.35 bp/Mb) [ 32 ] and lower than that of Monopterus albus (10,259 bp/Mb) [ 33 ].…”