Skip to content

Research at St Andrews

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

Research output: Contribution to journalArticle


Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold, David S. Portnoy

School/Research organisations


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.


Original languageEnglish
Article number163
Number of pages11
JournalBMC Genomics
Publication statusPublished - 23 Feb 2018

    Research areas

  • Linkage map, RADseq, Aquaculture, Synteny

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by journal

  1. STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus

    Espada, M., Eves-van den Akker, S., Maier, T., Vijayapalani, P., Baum, T., Mota, M. & Jones, J. T., 27 Jul 2018, In : BMC Genomics. 19, 553.

    Research output: Contribution to journalArticle

  2. Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

    Thorpe, P., Cock, P. J. A. & Bos, J., 2 Mar 2016, In : BMC Genomics. 17, 18 p., 172.

    Research output: Contribution to journalArticle

  3. The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

    Warne, B., Harkins, C. P., Harris, S. R., Vatsiou, A., Stanley-Wall, N., Parkhill, J., Peacock, S. J., Palmer, T. & Holden, M. T. G., 13 Mar 2016, In : BMC Genomics. 17, 1, p. 222

    Research output: Contribution to journalArticle

ID: 252804751