Abstract
BackgroundThe 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.ResultsWe 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.ConclusionThe 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.
Highlights
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
We show for the first time the gene expression profiles that support extreme anoxia tolerance and postdiapause development, as well as potential genes under positive selection in the A. limnaeus lineage compared to several teleost species
Estimation of genome size Flow cytometry quantification of propidium iodide fluorescence intensity yields an estimated genome size for A. limnaeus of 1.03 Gbp when Danio rerio and Gallus gallus free-nuclei were used as standards (Fig. 1)
Summary
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. Contrasting with the typical pattern of convergence and extension of the amoeboid (deep) embryonic blastomeres that is observed in most other teleost embryos during epiboly, deep blastomeres of A. limnaeus dissociate and migrate away from each other across the yolk surface during epiboly [18, 19] This process appears to temporally disconnect epiboly from germ layer formation in annual killifishes and these deep cells can remain dispersed across the yolk surface for several days before reaggregating and forming a definitive embryonic axis [16]. The biological significance and mechanism of this phenomenon are still unclear, it has been suggested that the spatial arrangement of embryonic cells in DI may allow damaged cells to be “sloughed” and replaced by surrounding pluripotent cells [12, 16] This phenomenon may be facilitated by unique expression of genes important for gastrulation [20]. Entrance into diapause is an alternative developmental trajectory that is unique biochemically, physiologically, and morphologically from escape embryos
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