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Citation for Study 22058

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

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

This study is part of submission 22058 (Status: Published).

Citation

Wagner J.T., Priya singh P., Romney A., Riggs C., Minx P., Woll S.C., Roush J., Warren W., Brunet A., & Podrabsky J. 2017. The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development. BMC Genomics, .

Authors

• Wagner J.T. (submitter) 5038109715
• Priya singh P.
• Romney A.
• Riggs C.
• Minx P.
• Woll S.C.
• Roush J.
• Warren W.
• Brunet A.
• Podrabsky J.

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 annual killifish biology. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and its impact on vertebrate physiology and evolution.

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S22058
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref27994,
  	 author = {Josiah Tad Wagner and Param  Priya Singh and Amie  Romney and Claire  Riggs and Patrick  Minx and Steven Cody Woll and Jake  Roush and Wesley  Warren and Anne  Brunet and Jason  Podrabsky},
  	 title = {The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development},
  	 year = {2017},
  	 keywords = {},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Genomics},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 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 annual killifish biology. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and its impact on vertebrate physiology and evolution.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 27994
  AU  - Wagner,Josiah Tad
  AU  - Priya Singh,Param 
  AU  - Romney,Amie 
  AU  - Riggs,Claire 
  AU  - Minx,Patrick 
  AU  - Woll,Steven Cody
  AU  - Roush,Jake 
  AU  - Warren,Wesley 
  AU  - Brunet,Anne 
  AU  - Podrabsky,Jason 
  T1  - The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development
  PY  - 2017
  KW  - 
  UR  - http://dx.doi.org/
  N2  - 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 annual killifish biology. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and its impact on vertebrate physiology and evolution.
  
  L3  - 
  JF  - BMC Genomics
  VL  - 
  IS  - 
  ER  -