Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Handle URI:
http://hdl.handle.net/10754/598911
Title:
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Authors:
Gan, Xiangchao; Stegle, Oliver; Behr, Jonas; Steffen, Joshua G.; Drewe, Philipp; Hildebrand, Katie L.; Lyngsoe, Rune; Schultheiss, Sebastian J.; Osborne, Edward J.; Sreedharan, Vipin T.; Kahles, André; Bohnert, Regina; Jean, Géraldine; Derwent, Paul; Kersey, Paul; Belfield, Eric J.; Harberd, Nicholas P.; Kemen, Eric; Toomajian, Christopher; Kover, Paula X.; Clark, Richard M.; Rätsch, Gunnar; Mott, Richard
Abstract:
Genetic differences between Arabidopsis thaliana accessions underlie the plants 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. ©2011 Macmillan Publishers Limited. All rights reserved.
Citation:
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419–423. Available: http://dx.doi.org/10.1038/nature10414.
Publisher:
Springer Nature
Journal:
Nature
KAUST Grant Number:
KUK-I1-002-03
Issue Date:
28-Aug-2011
DOI:
10.1038/nature10414
PubMed ID:
21874022
Type:
Article
ISSN:
0028-0836; 1476-4687
Sponsors:
We thank C. Jiang and C. Brown for technical help; P. Dikjwel, K. Schneeberger and D. Weigel for providing sequence data in advance of publication; and J. Flint, M. Tsiantis, E. Feil, L. Hurst, A. Wachter and D. Weigel for comments on the manuscript. Funding was provided by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/F022697/1 (to R. M. and P. X. K.), BB/D016029/2 (to P. X. K and R. M.), BB/F020759/1 (to N.P.H.) and BB/F019793/1 to P. K. (PI E. Birney), by core funding of the Max Planck Society (to G. R.), the German Research Foundation RA1894/1-1 and RA1894/2-1 (to G. R.), Volkswagen Stiftung (to O.S.), the National Science Foundation (NSF) 0929262 (to R. C. and C. T.) and 0820985 (to R. C., Principal Investigator L. Sieburth), and award no. KUK-I1-002-03 (to N.P.H), made by King Abdullah University of Science and Technology (KAUST). D. Buck, I. Ragoussis and colleagues in the Wellcome Trust Centre for Human Genetics Genomics Core performed most of the genomic sequencing, supported by the Wellcome Trust Core grant 090532/Z/09/Z. Contribution no. 11-388-J from the Kansas Agricultural Experiment Station.
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Full metadata record

DC FieldValue Language
dc.contributor.authorGan, Xiangchaoen
dc.contributor.authorStegle, Oliveren
dc.contributor.authorBehr, Jonasen
dc.contributor.authorSteffen, Joshua G.en
dc.contributor.authorDrewe, Philippen
dc.contributor.authorHildebrand, Katie L.en
dc.contributor.authorLyngsoe, Runeen
dc.contributor.authorSchultheiss, Sebastian J.en
dc.contributor.authorOsborne, Edward J.en
dc.contributor.authorSreedharan, Vipin T.en
dc.contributor.authorKahles, Andréen
dc.contributor.authorBohnert, Reginaen
dc.contributor.authorJean, Géraldineen
dc.contributor.authorDerwent, Paulen
dc.contributor.authorKersey, Paulen
dc.contributor.authorBelfield, Eric J.en
dc.contributor.authorHarberd, Nicholas P.en
dc.contributor.authorKemen, Ericen
dc.contributor.authorToomajian, Christopheren
dc.contributor.authorKover, Paula X.en
dc.contributor.authorClark, Richard M.en
dc.contributor.authorRätsch, Gunnaren
dc.contributor.authorMott, Richarden
dc.date.accessioned2016-02-25T13:43:34Zen
dc.date.available2016-02-25T13:43:34Zen
dc.date.issued2011-08-28en
dc.identifier.citationGan X, Stegle O, Behr J, Steffen JG, Drewe P, et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419–423. Available: http://dx.doi.org/10.1038/nature10414.en
dc.identifier.issn0028-0836en
dc.identifier.issn1476-4687en
dc.identifier.pmid21874022en
dc.identifier.doi10.1038/nature10414en
dc.identifier.urihttp://hdl.handle.net/10754/598911en
dc.description.abstractGenetic differences between Arabidopsis thaliana accessions underlie the plants 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. ©2011 Macmillan Publishers Limited. All rights reserved.en
dc.description.sponsorshipWe thank C. Jiang and C. Brown for technical help; P. Dikjwel, K. Schneeberger and D. Weigel for providing sequence data in advance of publication; and J. Flint, M. Tsiantis, E. Feil, L. Hurst, A. Wachter and D. Weigel for comments on the manuscript. Funding was provided by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/F022697/1 (to R. M. and P. X. K.), BB/D016029/2 (to P. X. K and R. M.), BB/F020759/1 (to N.P.H.) and BB/F019793/1 to P. K. (PI E. Birney), by core funding of the Max Planck Society (to G. R.), the German Research Foundation RA1894/1-1 and RA1894/2-1 (to G. R.), Volkswagen Stiftung (to O.S.), the National Science Foundation (NSF) 0929262 (to R. C. and C. T.) and 0820985 (to R. C., Principal Investigator L. Sieburth), and award no. KUK-I1-002-03 (to N.P.H), made by King Abdullah University of Science and Technology (KAUST). D. Buck, I. Ragoussis and colleagues in the Wellcome Trust Centre for Human Genetics Genomics Core performed most of the genomic sequencing, supported by the Wellcome Trust Core grant 090532/Z/09/Z. Contribution no. 11-388-J from the Kansas Agricultural Experiment Station.en
dc.publisherSpringer Natureen
dc.titleMultiple reference genomes and transcriptomes for Arabidopsis thalianaen
dc.typeArticleen
dc.identifier.journalNatureen
dc.contributor.institutionWellcome Trust Centre for Human Genetics, Oxford, United Kingdomen
dc.contributor.institutionMax Planck Institute for Developmental Biology, Tubingen, Germanyen
dc.contributor.institutionFriedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germanyen
dc.contributor.institutionUniversity of Utah, Salt Lake City, United Statesen
dc.contributor.institutionKansas State University, Manhattan, United Statesen
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdomen
dc.contributor.institutionEuropean Bioinformatics Institute, Cambridge, United Kingdomen
dc.contributor.institutionThe Sainsbury Laboratory, Norwich,en
dc.contributor.institutionUniversity of Bath, Bath, United Kingdomen
kaust.grant.numberKUK-I1-002-03en
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