title: The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
abstract: We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
authors.forename: Tina T
authors.initials: TT
authors.lastname: Hu
authors.forename: Pedro
authors.initials: P
authors.lastname: Pattyn
authors.forename: Erica G
authors.initials: EG
authors.lastname: Bakker
authors.forename: Jun
authors.initials: J
authors.lastname: Cao
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.forename: Richard M
authors.initials: RM
authors.lastname: Clark
authors.forename: Noah
authors.initials: N
authors.lastname: Fahlgren
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Fawcett
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.forename: Jesse D
authors.initials: JD
authors.lastname: Hollister
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.forename: Robert P
authors.initials: RP
authors.lastname: Ottilar
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.forename: Xi
authors.initials: X
authors.lastname: Wang
authors.forename: Liang
authors.initials: L
authors.lastname: Yang
authors.forename: Mikhail E
authors.initials: ME
authors.lastname: Nasrallah
authors.forename: Joy
authors.initials: J
authors.lastname: Bergelson
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
authors.forename: Brandon S
authors.initials: BS
authors.lastname: Gaut
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Ya-Long
authors.initials: YL
authors.lastname: Guo
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D002503:Centromere / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D018744:DNA, Plant