Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines

Basit Öğe Kaydı
dc.authorid0000-0003-3439-9921
dc.authorid0000-0003-2636-661X
dc.authorid0000-0002-2556-2478
dc.authorid0000-0002-2556-2478
dc.authorid0000-0002-2556-2478
dc.authorid0000-0002-0462-5775
dc.authorid0000-0002-8999-6785
dc.authorscopusid56371114900
dc.authorscopusid23768631700
dc.authorscopusid7005256791
dc.authorscopusid8501498100
dc.authorscopusid20336787400
dc.authorscopusid55772448500
dc.authorscopusid7003539101
dc.authorwosidMitchell-Olds, Thomas/K-8121-2012
dc.authorwosidFigueroa, Melania/R-7696-2017
dc.authorwosidBudak, Hikmet/U-8517-2019
dc.authorwosidBudak, Hikmet/F-4708-2010
dc.authorwosidBudak, Hikmet/S-5835-2017
dc.authorwosidMockler, Todd C/L-2609-2013
dc.authorwosidManzaneda, Antonio/AAG-1776-2019
dc.contributor.authorGordon, Sean P.
dc.contributor.authorPriest, Henry
dc.contributor.authorMarais, David L. Des
dc.contributor.authorSchackwitz, Wendy
dc.contributor.authorFigueroa, Melania
dc.contributor.authorMartin, Joel
dc.contributor.authorVogel, John P.
dc.contributor.authorTuna, Metin
dc.date.accessioned2022-05-11T14:45:47Z
dc.date.available2022-05-11T14:45:47Z
dc.date.issued2014
dc.departmentFakülteler, Ziraat Fakültesi, Tarla Bitkileri Bölümü
dc.description.abstractBrachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
dc.description.sponsorshipOffice of Science (BER), US Department of Energy, USDA NIFA; USDA CRISUnited States Department of Agriculture (USDA) [5325-21000-017-00]; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [0922457] Funding Source: National Science Foundation
dc.description.sponsorshipWe thank Uffe Hellsten for help with population genetics. Genomic DNA sequencing was performed at the US Department of Energy Joint Genome Institute through the Community Sequencing Program. Deep sequencing of the Bd1-1 transcriptome was performed at the Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR. This work was supported by the Office of Science (BER), US Department of Energy, USDA NIFA, and by the USDA CRIS project 5325-21000-017-00.
dc.identifier.doi10.1111/tpj.12569
dc.identifier.endpage374
dc.identifier.issn0960-7412
dc.identifier.issn1365-313X
dc.identifier.issue3en_US
dc.identifier.pmid24888695
dc.identifier.scopus2-s2.0-84905111430
dc.identifier.scopusqualityQ1
dc.identifier.startpage361
dc.identifier.urihttps://doi.org/10.1111/tpj.12569
dc.identifier.urihttps://hdl.handle.net/20.500.11776/10149
dc.identifier.volume79
dc.identifier.wosWOS:000340163500001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorTuna, Metin
dc.language.isoen
dc.publisherWiley
dc.relation.ispartofPlant Journal
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectBrachypodium distachyon
dc.subjectnatural diversity
dc.subjectgenome sequencing
dc.subjecttranscriptome
dc.subjectdrought
dc.subjectArabidopsis-Thaliana
dc.subjectModel System
dc.subjectDrought
dc.subjectStress
dc.subjectExpression
dc.subjectOverexpression
dc.subjectPatterns
dc.subjectReveals
dc.subjectRice
dc.subjectMap
dc.titleGenome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
dc.typeArticle

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
Küçük Resim
İsim:
10149.pdf
Boyut:
1.2 MB
Biçim:
Adobe Portable Document Format
Açıklama:
Tam Metin / Full Text
İndir

Koleksiyon

WoS İndeksli Yayınlar Koleksiyonu
PubMed İndeksli Yayın Koleksiyonu
Scopus İndeksli Yayınlar Koleksiyonu
Ziraat Fakültesi Koleksiyonu