De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

<h4>Background</h4>Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference t...

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Autores principales:	Jacqueline D Farrell, Stephen Byrne, Cristiana Paina, Torben Asp
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0dd96d0dd00c464385eada72d481db04
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spelling	oai:doaj.org-article:0dd96d0dd00c464385eada72d481db042021-11-25T06:04:27ZDe novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.1932-620310.1371/journal.pone.0103567https://doaj.org/article/0dd96d0dd00c464385eada72d481db042014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25126744/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.<h4>Result</h4>De novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.<h4>Conclusion</h4>Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.Jacqueline D FarrellStephen ByrneCristiana PainaTorben AspPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e103567 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jacqueline D Farrell Stephen Byrne Cristiana Paina Torben Asp De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
description	<h4>Background</h4>Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.<h4>Result</h4>De novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.<h4>Conclusion</h4>Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.
format	article
author	Jacqueline D Farrell Stephen Byrne Cristiana Paina Torben Asp
author_facet	Jacqueline D Farrell Stephen Byrne Cristiana Paina Torben Asp
author_sort	Jacqueline D Farrell
title	De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
title_short	De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
title_full	De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
title_fullStr	De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
title_full_unstemmed	De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
title_sort	de novo assembly of the perennial ryegrass transcriptome using an rna-seq strategy.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/0dd96d0dd00c464385eada72d481db04
work_keys_str_mv	AT jacquelinedfarrell denovoassemblyoftheperennialryegrasstranscriptomeusinganrnaseqstrategy AT stephenbyrne denovoassemblyoftheperennialryegrasstranscriptomeusinganrnaseqstrategy AT cristianapaina denovoassemblyoftheperennialryegrasstranscriptomeusinganrnaseqstrategy AT torbenasp denovoassemblyoftheperennialryegrasstranscriptomeusinganrnaseqstrategy
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De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

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