Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Xiangchao Gan, Oliver Stegle, Jonas Behr, Joshua G. Steffen, Philipp Drewe, Katie L. Hildebrand, Rune Lyngsoe, Sebastian J. Schultheiss, Edward J. Osborne, Vipin T. Sreedharan, André Kahles, Regina Bohnert, Géraldine Jean, Paul Derwent, Paul Kersey, Eric J. Belfield, Nicholas P. Harberd, Eric Kemen, Christopher Toomajian (), Paula X. Kover (), Richard M. Clark (), Gunnar Rätsch () and Richard Mott ()
Additional contact information
Xiangchao Gan: Wellcome Trust Centre for Human Genetics, University of Oxford
Oliver Stegle: Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, Spemannstraβe 38
Jonas Behr: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Joshua G. Steffen: University of Utah
Philipp Drewe: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Katie L. Hildebrand: Kansas State University
Rune Lyngsoe: University of Oxford
Sebastian J. Schultheiss: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Edward J. Osborne: University of Utah
Vipin T. Sreedharan: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
André Kahles: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Regina Bohnert: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Géraldine Jean: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Paul Derwent: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton
Paul Kersey: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton
Eric J. Belfield: University of Oxford
Nicholas P. Harberd: University of Oxford
Eric Kemen: The Sainsbury Laboratory
Christopher Toomajian: Kansas State University
Paula X. Kover: University of Bath
Richard M. Clark: University of Utah
Gunnar Rätsch: Friedrich Miescher Laboratory, Max Planck Society, Spemannstraβe 39
Richard Mott: Wellcome Trust Centre for Human Genetics, University of Oxford

Nature, 2011, vol. 477, issue 7365, 419-423

Abstract: 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.

Date: 2011
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DOI: 10.1038/nature10414

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