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The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there...

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Autores principales: Hammond, S. Austin, Warren, René L., Vandervalk, Benjamin P., Kucuk, Erdi, Khan, Hamza, Gibb, Ewan A., Pandoh, Pawan, Kirk, Heather, Zhao, Yongjun, Jones, Martin, Mungall, Andrew J., Coope, Robin, Pleasance, Stephen, Moore, Richard A., Holt, Robert A., Round, Jessica M., Ohora, Sara, Walle, Branden V., Veldhoen, Nik, Helbing, Caren C., Birol, Inanc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681567/
https://www.ncbi.nlm.nih.gov/pubmed/29127278
http://dx.doi.org/10.1038/s41467-017-01316-7
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author Hammond, S. Austin
Warren, René L.
Vandervalk, Benjamin P.
Kucuk, Erdi
Khan, Hamza
Gibb, Ewan A.
Pandoh, Pawan
Kirk, Heather
Zhao, Yongjun
Jones, Martin
Mungall, Andrew J.
Coope, Robin
Pleasance, Stephen
Moore, Richard A.
Holt, Robert A.
Round, Jessica M.
Ohora, Sara
Walle, Branden V.
Veldhoen, Nik
Helbing, Caren C.
Birol, Inanc
author_facet Hammond, S. Austin
Warren, René L.
Vandervalk, Benjamin P.
Kucuk, Erdi
Khan, Hamza
Gibb, Ewan A.
Pandoh, Pawan
Kirk, Heather
Zhao, Yongjun
Jones, Martin
Mungall, Andrew J.
Coope, Robin
Pleasance, Stephen
Moore, Richard A.
Holt, Robert A.
Round, Jessica M.
Ohora, Sara
Walle, Branden V.
Veldhoen, Nik
Helbing, Caren C.
Birol, Inanc
author_sort Hammond, S. Austin
collection PubMed
description Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research.
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spelling pubmed-56815672017-11-16 The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA Hammond, S. Austin Warren, René L. Vandervalk, Benjamin P. Kucuk, Erdi Khan, Hamza Gibb, Ewan A. Pandoh, Pawan Kirk, Heather Zhao, Yongjun Jones, Martin Mungall, Andrew J. Coope, Robin Pleasance, Stephen Moore, Richard A. Holt, Robert A. Round, Jessica M. Ohora, Sara Walle, Branden V. Veldhoen, Nik Helbing, Caren C. Birol, Inanc Nat Commun Article Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research. Nature Publishing Group UK 2017-11-10 /pmc/articles/PMC5681567/ /pubmed/29127278 http://dx.doi.org/10.1038/s41467-017-01316-7 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Hammond, S. Austin
Warren, René L.
Vandervalk, Benjamin P.
Kucuk, Erdi
Khan, Hamza
Gibb, Ewan A.
Pandoh, Pawan
Kirk, Heather
Zhao, Yongjun
Jones, Martin
Mungall, Andrew J.
Coope, Robin
Pleasance, Stephen
Moore, Richard A.
Holt, Robert A.
Round, Jessica M.
Ohora, Sara
Walle, Branden V.
Veldhoen, Nik
Helbing, Caren C.
Birol, Inanc
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title_full The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title_fullStr The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title_full_unstemmed The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title_short The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
title_sort north american bullfrog draft genome provides insight into hormonal regulation of long noncoding rna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681567/
https://www.ncbi.nlm.nih.gov/pubmed/29127278
http://dx.doi.org/10.1038/s41467-017-01316-7
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