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; Richard Mott

doi:10.1038/nature10414

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. KoverRichard M. Clark, Gunnar Rätsch, Richard Mott

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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.

Original language	English (US)
Pages (from-to)	419-423
Number of pages	5
Journal	Nature
Volume	477
Issue number	7365
DOIs	https://doi.org/10.1038/nature10414
State	Published - Aug 28 2011
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-002-03
Acknowledgements: 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.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., ... Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477(7365), 419-423. https://doi.org/10.1038/nature10414

@article{3ceaa59ced004815ba0cb50512abfdeb,

title = "Multiple reference genomes and transcriptomes for Arabidopsis thaliana",

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. {\textcopyright}2011 Macmillan Publishers Limited. All rights reserved.",

author = "Xiangchao Gan and Oliver Stegle and Jonas Behr and Steffen, {Joshua G.} and Philipp Drewe and Hildebrand, {Katie L.} and Rune Lyngsoe and Schultheiss, {Sebastian J.} and Osborne, {Edward J.} and Sreedharan, {Vipin T.} and Andr{\'e} Kahles and Regina Bohnert and G{\'e}raldine Jean and Paul Derwent and Paul Kersey and Belfield, {Eric J.} and Harberd, {Nicholas P.} and Eric Kemen and Christopher Toomajian and Kover, {Paula X.} and Clark, {Richard M.} and Gunnar R{\"a}tsch and Richard Mott",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-002-03 Acknowledgements: 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. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

year = "2011",

month = aug,

day = "28",

doi = "10.1038/nature10414",

language = "English (US)",

volume = "477",

pages = "419--423",

journal = "Nature",

issn = "0028-0836",

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}

Gan, X, Stegle, O, Behr, J, Steffen, JG, Drewe, P, Hildebrand, KL, Lyngsoe, R, Schultheiss, SJ, Osborne, EJ, Sreedharan, VT, Kahles, A, Bohnert, R, Jean, G, Derwent, P, Kersey, P, Belfield, EJ, Harberd, NP, Kemen, E, Toomajian, C, Kover, PX, Clark, RM, Rätsch, G & Mott, R 2011, 'Multiple reference genomes and transcriptomes for Arabidopsis thaliana', Nature, vol. 477, no. 7365, pp. 419-423. https://doi.org/10.1038/nature10414

TY - JOUR

T1 - Multiple reference genomes and transcriptomes for Arabidopsis thaliana

AU - Gan, Xiangchao

AU - Stegle, Oliver

AU - Behr, Jonas

AU - Steffen, Joshua G.

AU - Drewe, Philipp

AU - Hildebrand, Katie L.

AU - Lyngsoe, Rune

AU - Schultheiss, Sebastian J.

AU - Osborne, Edward J.

AU - Sreedharan, Vipin T.

AU - Kahles, André

AU - Bohnert, Regina

AU - Jean, Géraldine

AU - Derwent, Paul

AU - Kersey, Paul

AU - Belfield, Eric J.

AU - Harberd, Nicholas P.

AU - Kemen, Eric

AU - Toomajian, Christopher

AU - Kover, Paula X.

AU - Clark, Richard M.

AU - Rätsch, Gunnar

AU - Mott, Richard

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-002-03 Acknowledgements: 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. This publication acknowledges KAUST support, but has no KAUST affiliated authors.

PY - 2011/8/28

Y1 - 2011/8/28

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/598911

UR - http://www.nature.com/articles/nature10414

UR - http://www.scopus.com/inward/record.url?scp=80053132716&partnerID=8YFLogxK

U2 - 10.1038/nature10414

DO - 10.1038/nature10414

M3 - Article

C2 - 21874022

SN - 0028-0836

VL - 477

SP - 419

EP - 423

JO - Nature

JF - Nature

IS - 7365

ER -

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Abstract

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