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Transcriptomics of diapause in an isogenic self-fertilizing vertebrate

BACKGROUND: Many vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Identification of diapause genes has been challenging due in part to the genetic heterogeneity of most vertebrate animals. RESULTS: Here we take...

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Autores principales: Mesak, Felix, Tatarenkov, Andrey, Avise, John C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4657215/
https://www.ncbi.nlm.nih.gov/pubmed/26597228
http://dx.doi.org/10.1186/s12864-015-2210-0
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author Mesak, Felix
Tatarenkov, Andrey
Avise, John C.
author_facet Mesak, Felix
Tatarenkov, Andrey
Avise, John C.
author_sort Mesak, Felix
collection PubMed
description BACKGROUND: Many vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Identification of diapause genes has been challenging due in part to the genetic heterogeneity of most vertebrate animals. RESULTS: Here we take the advantage of the mangrove rivulus fish (Kryptolebias marmoratus or Kmar)—the only vertebrate that is extremely inbred due to consistent self-fertilization—to generate isogenic lineages for transcriptomic dissection. Because the Kmar genome is not publicly available, we built de novo genomic (642 Mb) and transcriptomic assemblies to serve as references for global genetic profiling of diapause in Kmar, via RNA-Seq. Transcripts unique to diapause in Kmar proved to constitute only a miniscule fraction (0.1 %) of the total pool of transcribed products. Most genes displayed lower expression in diapause than in post-diapause. However, some genes (notably dusp27, klhl38 and sqstm1) were significantly up-regulated during diapause, whereas others (col9a1, dspp and fmnl1) were substantially down-regulated, compared to both pre-diapause and post-diapause. CONCLUSION: Kmar offers a strong model for understanding patterns of gene expression during diapause. Our study highlights the importance of using a combination of genome and transcriptome assemblies as references for NGS-based RNA-Seq analyses. As for all identified diapause genes, in future studies it will be critical to link various levels of RNA expression with the functional roles of the coded products. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2210-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-46572152015-11-25 Transcriptomics of diapause in an isogenic self-fertilizing vertebrate Mesak, Felix Tatarenkov, Andrey Avise, John C. BMC Genomics Research Article BACKGROUND: Many vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Identification of diapause genes has been challenging due in part to the genetic heterogeneity of most vertebrate animals. RESULTS: Here we take the advantage of the mangrove rivulus fish (Kryptolebias marmoratus or Kmar)—the only vertebrate that is extremely inbred due to consistent self-fertilization—to generate isogenic lineages for transcriptomic dissection. Because the Kmar genome is not publicly available, we built de novo genomic (642 Mb) and transcriptomic assemblies to serve as references for global genetic profiling of diapause in Kmar, via RNA-Seq. Transcripts unique to diapause in Kmar proved to constitute only a miniscule fraction (0.1 %) of the total pool of transcribed products. Most genes displayed lower expression in diapause than in post-diapause. However, some genes (notably dusp27, klhl38 and sqstm1) were significantly up-regulated during diapause, whereas others (col9a1, dspp and fmnl1) were substantially down-regulated, compared to both pre-diapause and post-diapause. CONCLUSION: Kmar offers a strong model for understanding patterns of gene expression during diapause. Our study highlights the importance of using a combination of genome and transcriptome assemblies as references for NGS-based RNA-Seq analyses. As for all identified diapause genes, in future studies it will be critical to link various levels of RNA expression with the functional roles of the coded products. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2210-0) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-23 /pmc/articles/PMC4657215/ /pubmed/26597228 http://dx.doi.org/10.1186/s12864-015-2210-0 Text en © Mesak et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Mesak, Felix
Tatarenkov, Andrey
Avise, John C.
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title_full Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title_fullStr Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title_full_unstemmed Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title_short Transcriptomics of diapause in an isogenic self-fertilizing vertebrate
title_sort transcriptomics of diapause in an isogenic self-fertilizing vertebrate
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4657215/
https://www.ncbi.nlm.nih.gov/pubmed/26597228
http://dx.doi.org/10.1186/s12864-015-2210-0
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