ArticleBMC genomics2017
De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 28 citations in OpenAlex.
- The Genome of Apera spica-venti: A Major Grass Weed.Genome biology and evolution · 2025Article
- Weed biology and management in the multi-omics era: Progress and perspectives.Plant communications · 2024Review
- Optimization and application of non-native Phragmites australis transcriptome assemblies.PloS one · 2023Article
- Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses.Pathogens (Basel, Switzerland) · 2022Article
- GW10, a member of P450 subfamily regulates grain size and grain number in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- The analysis of reference genes expression stability in susceptible and resistant Apera spica-venti populations under herbicide treatment.Scientific reports · 2021Article
- Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts.BMC genomics · 2019Article
- Defenses Against ROS in Crops and Weeds: The Effects of Interference and Herbicides.International journal of molecular sciences · 2019Review
- HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine.Scientific reports · 2019Article
- Full-Length Transcriptome Survey and Expression Analysis ofInternational journal of molecular sciences · 2018Article
- High QualityFrontiers in molecular biosciences · 2018Article
- Fitness of ALS-Inhibitors Herbicide Resistant Population of Loose Silky Bentgrass (Frontiers in plant science · 2017Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLoose 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.
resultsEight 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.
conclusionsDe 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.
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