Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)
Abstract
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.
- Authors:
-
- Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology and Center for Genome Research and Biocomputing
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute
- Portland State Univ., OR (United States). Dept. of Biology
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1628600
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Applications in Plant Science
- Additional Journal Information:
- Journal Volume: 1; Journal Issue: 3; Journal ID: ISSN 2168-0450
- Publisher:
- Botanical Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plant Sciences; Brachypodium sylvaticum; comparative genomics; de novo transcriptome; invasive species; simple sequence repeat (SSR); single-nucleotide polymorphism (SNP)
Citation Formats
Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). United States: N. p., 2013.
Web. doi:10.3732/apps.1200011.
Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., & Jaiswal, Pankaj. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). United States. https://doi.org/10.3732/apps.1200011
Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj. Tue .
"Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)". United States. https://doi.org/10.3732/apps.1200011. https://www.osti.gov/servlets/purl/1628600.
@article{osti_1628600,
title = {Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)},
author = {Fox, Samuel E. and Preece, Justin and Kimbrel, Jeffrey A. and Marchini, Gina L. and Sage, Abigail and Youens-Clark, Ken and Cruzan, Mitchell B. and Jaiswal, Pankaj},
abstractNote = {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.},
doi = {10.3732/apps.1200011},
journal = {Applications in Plant Science},
number = 3,
volume = 1,
place = {United States},
year = {Tue Mar 05 00:00:00 EST 2013},
month = {Tue Mar 05 00:00:00 EST 2013}
}
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