title: Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Xiangchao
authors.initials: X
authors.lastname: Gan
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.forename: Jonas
authors.initials: J
authors.lastname: Behr
authors.forename: Joshua G
authors.initials: JG
authors.lastname: Steffen
authors.forename: Philipp
authors.initials: P
authors.lastname: Drewe
authors.forename: Katie L
authors.initials: KL
authors.lastname: Hildebrand
authors.forename: Rune
authors.initials: R
authors.lastname: Lyngsoe
authors.forename: Sebastian J
authors.initials: SJ
authors.lastname: Schultheiss
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Osborne
authors.forename: Vipin T
authors.initials: VT
authors.lastname: Sreedharan
authors.forename: André
authors.initials: A
authors.lastname: Kahles
authors.forename: Regina
authors.initials: R
authors.lastname: Bohnert
authors.forename: Géraldine
authors.initials: G
authors.lastname: Jean
authors.forename: Paul
authors.initials: P
authors.lastname: Derwent
authors.forename: Paul
authors.initials: P
authors.lastname: Kersey
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Belfield
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Harberd
authors.forename: Eric
authors.initials: E
authors.lastname: Kemen
authors.forename: Christopher
authors.initials: C
authors.lastname: Toomajian
authors.forename: Paula X
authors.initials: PX
authors.lastname: Kover
authors.forename: Richard M
authors.initials: RM
authors.lastname: Clark
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
authors.forename: Richard
authors.initials: R
authors.lastname: Mott
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D006239:Haplotypes / Q000235:genetics; D054643:INDEL Mutation / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D020543:Proteome / Q000235:genetics; D036226:Seedlings / Q000235:genetics; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D020543:Proteome