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De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages

BACKGROUND: Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology an...

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Autores principales: Babineau, Marielle, Mahmood, Khalid, Mathiassen, Solvejg K., Kudsk, Per, Kristensen, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294808/
https://www.ncbi.nlm.nih.gov/pubmed/28166737
http://dx.doi.org/10.1186/s12864-017-3538-4
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author Babineau, Marielle
Mahmood, Khalid
Mathiassen, Solvejg K.
Kudsk, Per
Kristensen, Michael
author_facet Babineau, Marielle
Mahmood, Khalid
Mathiassen, Solvejg K.
Kudsk, Per
Kristensen, Michael
author_sort Babineau, Marielle
collection PubMed
description BACKGROUND: Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified. RESULTS: Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively. CONCLUSIONS: De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3538-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-52948082017-02-09 De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages Babineau, Marielle Mahmood, Khalid Mathiassen, Solvejg K. Kudsk, Per Kristensen, Michael BMC Genomics Research Article BACKGROUND: Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified. RESULTS: Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively. CONCLUSIONS: De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3538-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-06 /pmc/articles/PMC5294808/ /pubmed/28166737 http://dx.doi.org/10.1186/s12864-017-3538-4 Text en © The Author(s). 2017 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
Babineau, Marielle
Mahmood, Khalid
Mathiassen, Solvejg K.
Kudsk, Per
Kristensen, Michael
De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title_full De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title_fullStr De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title_full_unstemmed De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title_short De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages
title_sort de novo transcriptome assembly analysis of weed apera spica-venti from seven tissues and growth stages
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294808/
https://www.ncbi.nlm.nih.gov/pubmed/28166737
http://dx.doi.org/10.1186/s12864-017-3538-4
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