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Title: Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Journal Article · · Applications in Plant Science
DOI:https://doi.org/10.3732/apps.1200011· OSTI ID:1628600
 [1];  [1];  [2];  [3];  [1];  [4];  [3];  [1]
  1. Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology and Center for Genome Research and Biocomputing
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute
  3. Portland State Univ., OR (United States). Dept. of Biology
  4. Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
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Premise 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 Results: More 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. Conclusions: To 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.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI ID:
1628600
Journal Information:
Applications in Plant Science, Vol. 1, Issue 3; ISSN 2168-0450
Publisher:
Botanical Society of AmericaCopyright Statement
Country of Publication:
United States
Language:
English

References (26)

Plant communities in broad-leaved deciduous forests in Hordaland county, Western Norway journal August 2000
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics journal January 2008
Construction and analysis of a BAC library in the grass Brachypodium sylvaticum : its use as a tool to bridge the gap between rice and wheat in elucidating gene content journal March 2004
High-throughput functional annotation and data mining with the Blast2GO suite journal April 2008
Full-length transcriptome assembly from RNA-Seq data without a reference genome journal May 2011
Context-dependent pattern and process: the distribution and competitive dynamics of an invasive grass, Brachypodium sylvaticum journal November 2009
The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers journal June 2012
Species for Seeding Mountain Rangelands in Southeastern Idaho, Northeastern Utah, and Western Wyoming journal March 1974
InterPro in 2011: new developments in the family and domain prediction database journal November 2011
Changes in the ground flora in Wytham Woods, southern England from 1974 to 1991 - implications for nature conservation journal February 2000
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome journal January 2009
Why forests appear resistant to exotic plant invasions: intentional introductions, stand dynamics, and the role of shade tolerance journal April 2009
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor journal June 2010
Exploiting the Brachypodium Tool Box in cereal and grass research journal May 2011
Acclimation of photosynthesis to irradiance and spectral quality in British plant species: chlorophyll content, photosynthetic capacity and habitat preference journal April 1997
Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum) journal January 2012
Evidence for multiple sources of invasion and intraspecific hybridization in Brachypodium sylvaticum (Hudson) Beauv. in North America journal November 2008
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels journal February 2012
Selectively eliminating and conserving exotic plants to save an endangered butterfly from local extinction journal December 2008
Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential journal August 2001
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers journal November 2011
Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology journal March 2012
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) journal December 2010
Strategies for transcriptome analysis in nonmodel plants journal February 2012
Compact genomes and complex evolution in the genus Brachypodium journal December 2010
Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana journal January 2012

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RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification journal June 2019
De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum journal May 2014
PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers journal June 2016
Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution journal November 2019
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification text January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
plant Sciences
Brachypodium sylvaticum
comparative genomics
de novo transcriptome
invasive species
simple sequence repeat (SSR)
single-nucleotide polymorphism (SNP)