The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

BMC Genomics. 2018 Feb 20;19(1):155. doi: 10.1186/s12864-018-4539-7.

Abstract

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection.

Conclusion: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.

Keywords: Annual killifish; Austrofundulus limnaeus; Development; Fish genome; Gene expression; Positive selection; Stress tolerance; Transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Biological / genetics*
  • Animals
  • Base Composition
  • Biological Evolution
  • Chickens
  • Embryo, Nonmammalian
  • Embryonic Development / genetics*
  • Gene Expression Regulation
  • Genome Size
  • Genome*
  • Genomics / methods
  • Killifishes / embryology*
  • Killifishes / genetics
  • Killifishes / physiology*
  • Mitochondria / genetics
  • Mitochondria / metabolism
  • Phylogeny
  • Repetitive Sequences, Nucleic Acid
  • Stress, Physiological / genetics*
  • Vertebrates
  • Zebrafish