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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];  [2];  [3];  [4];  [2];  [5];  [4];  [2]
  1. Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology and Center for Genome Research and Biocomputing; DOE/OSTI
  2. Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology and Center for Genome Research and Biocomputing
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute
  4. Portland State Univ., OR (United States). Dept. of Biology
  5. 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 Laboratory (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, Journal Name: Applications in Plant Science Journal Issue: 3 Vol. 1; ISSN 2168-0450
Publisher:
Botanical Society of AmericaCopyright Statement
Country of Publication:
United States
Language:
English

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De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum journal May 2014
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Related Subjects

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