Publication Date:
2011-08-30
Description:
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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉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, Andre -- Bohnert, Regina -- Jean, Geraldine -- Derwent, Paul -- Kersey, Paul -- Belfield, Eric J -- Harberd, Nicholas P -- Kemen, Eric -- Toomajian, Christopher -- Kover, Paula X -- Clark, Richard M -- Ratsch, Gunnar -- Mott, Richard -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- BB/D016029/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F019793/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F020759/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F022697/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Aug 28;477(7365):419-23. doi: 10.1038/nature10414.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21874022" target="_blank"〉PubMed〈/a〉
Keywords:
Arabidopsis/classification/*genetics
;
Arabidopsis Proteins/genetics
;
Base Sequence
;
*Gene Expression Profiling
;
Gene Expression Regulation, Plant/*genetics
;
Genes, Plant/genetics
;
Genome, Plant/*genetics
;
Genomics
;
Haplotypes/genetics
;
INDEL Mutation/genetics
;
Molecular Sequence Annotation
;
Phylogeny
;
Polymorphism, Single Nucleotide/genetics
;
Proteome/genetics
;
Seedlings/genetics
;
Sequence Analysis, DNA
;
Transcription, Genetic/*genetics
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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