ArticleApplications in plant sciences2013
Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae).
Article in Applications in plant sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 34 citations in OpenAlex.
- Trends in the evolution of intronless genes inFrontiers in plant science · 2023Article
- Scripting Analyses of Genomes in Ensembl Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera.Scientific data · 2021Article
- Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.Nucleic acids research · 2021Article
- Comparatively Barcoded Chromosomes ofInternational journal of molecular sciences · 2019Article
- RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification.BMC genomics · 2019Article
- Trait divergence, not plasticity, determines the success of a newly invasive plant.Annals of botany · 2019Article
- Gramene 2018: unifying comparative genomics and pathway resources for plant research.Nucleic acids research · 2018Article
- Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq.Frontiers in plant science · 2017Article
- Genomics of crop wild relatives: expanding the gene pool for crop improvement.Plant biotechnology journal · 2016Review
- Gramene 2016: comparative plant genomics and pathway resources.Nucleic acids research · 2016Article
- PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers.Frontiers in plant science · 2016Article
- Shoot transcriptome of the giant reed, Arundo donax.Data in brief · 2015Article
- Using soil seed banks to assess temporal patterns of genetic variation in invasive plant populations.Ecology and evolution · 2014Article
- De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.PloS one · 2014Article
- Gramene 2013: comparative plant genomics resources.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledPREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. • METHODS AND
resultsMore than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. •
conclusionsTo our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.