The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

Joanna L Kelley; Muh-Ching Yee; Anthony P Brown; Rhea R Richardson; Andrey Tatarenkov; Clarence C Lee; Timothy T Harkins; Carlos D Bustamante; Ryan L Earley

doi:10.1093/gbe/evw145

The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

Genome Biol Evol. 2016 Aug 16;8(7):2145-54. doi: 10.1093/gbe/evw145.

Authors

Joanna L Kelley¹, Muh-Ching Yee², Anthony P Brown³, Rhea R Richardson⁴, Andrey Tatarenkov⁵, Clarence C Lee⁶, Timothy T Harkins⁶, Carlos D Bustamante⁴, Ryan L Earley⁷

Affiliations

¹ School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington joanna.l.kelley@wsu.edu.
² Department of Plant Biology, Carnegie Institution for Science, Stanford, California.
³ School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington.
⁴ Department of Genetics, Stanford University, Stanford, California.
⁵ Department of Ecology and Evolutionary Biology, University of California, Irvine, California.
⁶ Thermo Fisher Scientific, Carlsbad, California.
⁷ Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama.

Abstract

The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology.

Keywords: fish; genome; hermaphrodite; isogenic; mangrove rivulus.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Adaptation, Physiological*
Animals
Cyprinodontiformes / genetics*
Extreme Environments*
Female
Genetic Variation*
Genome*
Male
Molecular Sequence Annotation
Phenotype*

Grants and funding

F32 GM087069/GM/NIGMS NIH HHS/United States