Transcriptome-Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management

The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.

Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BACKGROUND

The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome.

RESULTS

Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (F_ST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis.

CONCLUSION

This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.