De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Abstract Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spin...

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Autores principales:	Jared Mamrot, Roxane Legaie, Stacey J. Ellery, Trevor Wilson, Torsten Seemann, David R. Powell, David K. Gardner, David W. Walker, Peter Temple-Smith, Anthony T. Papenfuss, Hayley Dickinson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9bc90ddf082f424da5785dbce52a8b31
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spelling	oai:doaj.org-article:9bc90ddf082f424da5785dbce52a8b312021-12-02T11:53:01ZDe novo transcriptome assembly for the spiny mouse (Acomys cahirinus)10.1038/s41598-017-09334-72045-2322https://doaj.org/article/9bc90ddf082f424da5785dbce52a8b312017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-09334-7https://doaj.org/toc/2045-2322Abstract Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.Jared MamrotRoxane LegaieStacey J. ElleryTrevor WilsonTorsten SeemannDavid R. PowellDavid K. GardnerDavid W. WalkerPeter Temple-SmithAnthony T. PapenfussHayley DickinsonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jared Mamrot Roxane Legaie Stacey J. Ellery Trevor Wilson Torsten Seemann David R. Powell David K. Gardner David W. Walker Peter Temple-Smith Anthony T. Papenfuss Hayley Dickinson De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
description	Abstract Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.
format	article
author	Jared Mamrot Roxane Legaie Stacey J. Ellery Trevor Wilson Torsten Seemann David R. Powell David K. Gardner David W. Walker Peter Temple-Smith Anthony T. Papenfuss Hayley Dickinson
author_facet	Jared Mamrot Roxane Legaie Stacey J. Ellery Trevor Wilson Torsten Seemann David R. Powell David K. Gardner David W. Walker Peter Temple-Smith Anthony T. Papenfuss Hayley Dickinson
author_sort	Jared Mamrot
title	De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
title_short	De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
title_full	De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
title_fullStr	De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
title_full_unstemmed	De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
title_sort	de novo transcriptome assembly for the spiny mouse (acomys cahirinus)
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/9bc90ddf082f424da5785dbce52a8b31
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De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

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