Multiple reference genomes and transcriptomes for Arabidopsis thaliana

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dc.contributor.author Gan, Xiangchao
dc.contributor.author Stegle, Oliver
dc.contributor.author Behr, Jonas
dc.contributor.author Steffen, Joshua G.
dc.contributor.author Drewe, Philipp
dc.contributor.author Hildebrand, Katie L.
dc.contributor.author Lyngsoe, Rune
dc.contributor.author Schultheiss, Sebastian J.
dc.contributor.author Osborne, Edward J.
dc.contributor.author Sreedharan, Vipin T.
dc.contributor.author Kahles, André
dc.contributor.author Bohnert, Regina
dc.contributor.author Jean, Géraldine
dc.contributor.author Derwent, Paul
dc.contributor.author Kersey, Paul
dc.contributor.author Belfield, Eric J.
dc.contributor.author Harberd, Nicholas P.
dc.contributor.author Kemen, Eric
dc.contributor.author Toomajian, Christopher
dc.contributor.author Kover, Paula X.
dc.contributor.author Clark, Richard M.
dc.contributor.author Rätsch, Gunnar
dc.contributor.author Mott, Richard
dc.date.accessioned 2014-02-18T22:38:55Z
dc.date.available 2014-02-18T22:38:55Z
dc.date.issued 2014-02-18
dc.identifier.uri http://hdl.handle.net/2097/17179
dc.description.abstract Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions. en_US
dc.language.iso en_US en_US
dc.relation.uri http://www.nature.com/nature/journal/v477/n7365/full/nature10414.html en_US
dc.rights This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence, and is freely available to all readers at www.nature.com/nature . en_US
dc.subject Arabidopsis thaliana en_US
dc.subject Phenotypic variation en_US
dc.subject Gene expression en_US
dc.title Multiple reference genomes and transcriptomes for Arabidopsis thaliana en_US
dc.type Article (publisher version) en_US
dc.date.published 2011 en_US
dc.citation.doi doi:10.1038/nature10414 en_US
dc.citation.epage 423 en_US
dc.citation.issue 7365 en_US
dc.citation.jtitle Nature en_US
dc.citation.spage 419 en_US
dc.citation.volume 477 en_US
dc.contributor.authoreid toomajia en_US


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