Developing a high-quality linkage map for the atlantic killifish Fundulus heteroclitus

Jeffrey T. Miller, Noah M. Reid, Diane E. Nacci, Andrew Whitehead

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Killifish (Fundulus heteroclitus) are widely distributed among different aquatic environments where they demonstrate an impressive range of highly-plastic and locally adaptive phenotypes. High-throughput sequencing has begun to unravel the mechanisms and evolutionary history of these interesting features by establishing relationships in the genotype-phenotype map. However, some genotype-phenotype analyses require a higher order of contiguity than what initial scaffolded (fragmented genome assembly where contigs have been assemble into scaffolds) genome assemblies can provide. Here, we used 5,685 high-quality RAD-Seq markers from a single mapping family to order 84% of the scaffolded genome assembly to 24 chromosomes. This serves to: 1) expand the killifish genomic toolkit, 2) estimate genome-wide recombination rates, and 3) compare genome synteny to humans and other fishes. After initially building our map, we found that the selection of thresholds for sequence data filtration highly impacted scaffold placement in the map. We outline each step of the approach that dramatically improved our map to help guide others toward more effective linkage mapping for genome assembly. Our final map supports strong conservation of genomic synteny among closely related fish species and reveals previously described chromosomal rearrangements between more distantly related clades. However, we also commonly found minor scaffold misorientations in F. heteroclitus and in other assemblies, suggesting that further mapping (such as optical mapping) is necessary for finer scale resolution of genome structure. Lastly, we discuss the problems that would be expected from misoriented/ unplaced scaffolds and stress the importance of a quality mapped genome as a key feature for further investigating population and comparative genomic questions with F. heteroclitus and other taxa.

Original languageEnglish (US)
Pages (from-to)2851-2862
Number of pages12
JournalG3: Genes, Genomes, Genetics
Issue number9
StatePublished - Sep 1 2019

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Environmental Health Sciences [1R01ES021934-01 to A.W.]; and the National Science Foundation [OCE-1314567, DEB-1265282 to A.W.]. This research was also supported in part by the Postdoctoral Research Program at the U.S. Environmental Protection (US EPA) Office of Research and Development administered by the Oak Ridge Institute for Science and Education (ORISE) through Interagency Agreement No. DW92429801 between the U.S. Department of Energy and the US EPA. The views expressed in this article are those of the authors and do not necessarily represent the views or policies of the US EPA.

Publisher Copyright:
Copyright © 2019 Miller et al.


  • Atlantic Killifish
  • Genome synteny
  • Meiotic linkage map
  • RAD-Seq
  • Scaffold inversions


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