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

BMC Genomics
Josiah T WagnerJason E Podrabsky

Abstract

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. 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. The A. limnaeus ...Continue Reading

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Citations

Jun 5, 2019·The Journal of Experimental Biology·Josiah T WagnerJason E Podrabsky
Sep 8, 2018·Scientific Reports·Amie L T Romney, Jason E Podrabsky
Jun 20, 2020·Integrative and Comparative Biology·Emma L WeitznerAllyson G Hindle
Dec 26, 2019·Scientific Reports·Claire L RiggsJason E Podrabsky
Nov 30, 2018·Proceedings of the National Academy of Sciences of the United States of America·Christoph Englert
Feb 28, 2019·Frontiers in Endocrinology·Joan Carles Balasch, Lluís Tort
Nov 18, 2018·Proceedings of the National Academy of Sciences of the United States of America·Amie L T RomneyJason E Podrabsky
Aug 30, 2020·The Journal of Experimental Biology·Daniel E Zajic, Jason E Podrabsky
Feb 26, 2019·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Claire L RiggsJason E Podrabsky
Aug 12, 2020·The Journal of Experimental Biology·Daniel E ZajicJason E Podrabsky
Oct 26, 2021·The Journal of Animal Ecology·Katharina C Wollenberg ValeroKenneth B Storey

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Methods Mentioned

BETA
environmental stress
RNA-seq
flow cytometry
RNAseq
Illumina sequencing
Assay
electrophoresis
Hi-Seq

Software Mentioned

GUIDANCE
Allpaths
R Bioconductor package
control
Trimmomatic
Ensembl
PRANK
GenomicAlignments
_ Scaffolder
MAFFT

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