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

التفاصيل البيبلوغرافية
العنوان: The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.
المؤلفون: Wagner JT; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA. wagnejos@ohsu.edu.; Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon, USA. wagnejos@ohsu.edu., Singh PP; Department of Genetics, Stanford University, Stanford, California, USA., Romney AL; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA., Riggs CL; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA., Minx P; McDonnell Genome Institute at Washington University, St Louis, Missouri, USA., Woll SC; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA., Roush J; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA., Warren WC; McDonnell Genome Institute at Washington University, St Louis, Missouri, USA., Brunet A; Department of Genetics, Stanford University, Stanford, California, USA.; Glenn Center for the Biology of Aging, Stanford, California, USA., Podrabsky JE; Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA.
المصدر: BMC genomics [BMC Genomics] 2018 Feb 20; Vol. 19 (1), pp. 155. Date of Electronic Publication: 2018 Feb 20.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Genome*, Adaptation, Biological/*genetics , Embryonic Development/*genetics , Killifishes/*embryology , Killifishes/*physiology , Stress, Physiological/*genetics, Animals ; Base Composition ; Biological Evolution ; Chickens ; Embryo, Nonmammalian ; Gene Expression Regulation ; Genome Size ; Genomics/methods ; Killifishes/genetics ; Mitochondria/genetics ; Mitochondria/metabolism ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Vertebrates ; Zebrafish
مستخلص: 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.
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معلومات مُعتمدة: R24 OD011198 United States OD NIH HHS; R24 RR032658 United States RR NCRR NIH HHS; CEHG Fellowship International Stanford University; IOS-1354549 International National Science Foundation
فهرسة مساهمة: Keywords: Annual killifish; Austrofundulus limnaeus; Development; Fish genome; Gene expression; Positive selection; Stress tolerance; Transcriptome
تواريخ الأحداث: Date Created: 20180222 Date Completed: 20180827 Latest Revision: 20210729
رمز التحديث: 20240829
مُعرف محوري في PubMed: PMC5819677
DOI: 10.1186/s12864-018-4539-7
PMID: 29463212
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-018-4539-7