Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma

Abstract

Background: Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome.

Results: The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map.

Conclusions: The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.

Keywords: Aquaculture; Linkage map; RADseq; Synteny.

Fig. 1

Circular ideogram depicting locations of identified syntenic blocks on the southern flounder consensus linkage map. Black rectangles represent southern flounder linkage groups. Black ticks on the outside indicate location of loci on the southern flounder linkage map; loci mapped to the same location are stacked. Colored segments on the inside represent syntenic blocks identified in comparisons of southern flounder sequences to genome sequences of Japanese flounder (blue), European seabass (green), barramundi (olive), fugu (dark blue), green spotted puffer (purple), nile tilapia (orange), and three-spined stickleback (red)

Fig. 2

Comparative view of location of syntenic blocks on consensus linkage map of southern flounder and Japanese flounder. Solid black rectangles represent chromosomes of Japanese flounder. Black ticks indicate the positions of loci mapped on southern flounder linkage groups (colored rectangles); loci mapped to the same location are stacked. Syntenic blocks are connected by ribbons; the color corresponds to the color of each southern flounder linkage group. Width of the ribbon is proportional to the size of the syntenic block on a linkage group and its corresponding location on the chromosome of each comparison species

Fig. 3

Comparative view of location of syntenic blocks on consensus linkage map of southern flounder and three-spined stickleback. Solid black rectangles represent chromosomes of three-spined stickleback. Black ticks indicate the positions of loci mapped on southern flounder linkage groups (colored rectangles); loci mapped to the same location on the linkage map are stacked. Syntenic blocks are connected by ribbons; the color corresponds to the color of each linkage group. Width of the ribbon represents size of the syntenic block on a linkage group and its corresponding location on the chromosome of each comparison species

Fig. 4

Circular ideogram showing locations of synteny mapped transcripts and QTLs. Black rectangles represent southern flounder linkage groups. The location of QTLs identified in Japanese flounder are indicated by red (QTL for resistance to lymphocystis [30]), orange (QTL for resistance to Edwardsiella tarda [31]), and yellow (QTLs for growth; qWi-f14–1, qWi-f14–2 and qWe-f14, [64]).Genes identified as being significantly up- or down-regulated in European flounder when exposed to pollutants [33] are represented in blue inside the circle; genes identified as being differentially expressed in the context of salinity differences [32] are indicated in green outside the circle. Relative height of bars represents number of transcripts mapped to a single location