Home LiteratureArticle Details
PMID: 21478890 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.

Nature genetics ·Vol. 43 ·No. 5 ·2011-05-00 ·Pages 476-81

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL

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.

MeSH Terms
Arabidopsis/classification,genetics Base Sequence Centromere/genetics Chromosomes, Plant/genetics DNA, Plant/genetics Evolution, Molecular Genome, Plant Models, Genetic Molecular Sequence Data Sequence Homology, Nucleic Acid Species Specificity
Chemicals
DNA, Plant
Authors & Affiliations
30 authors, click to expand affiliations / ORCID
Hu Tina T
Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
Pattyn Pedro
Bakker Erica G
Cao Jun
Cheng Jan-Fang
Clark Richard M
Fahlgren Noah
Fawcett Jeffrey A
Grimwood Jane
Gundlach Heidrun
Haberer Georg
Hollister Jesse D
Ossowski Stephan
Ottilar Robert P
Salamov Asaf A
Schneeberger Korbinian
Spannagl Manuel
Wang Xi
Yang Liang
Nasrallah Mikhail E
Bergelson Joy
Carrington James C
Gaut Brandon S
Schmutz Jeremy
Mayer Klaus F X
Van de Peer Yves
Grigoriev Igor V
Nordborg Magnus
Weigel Detlef
Guo Ya-Long
References (62)
62 references, click to expand
  1. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants.
    Genome Res. 2006 Aug;16(8):1017-30 PMID: 16825662
  2. Transposed genes in Arabidopsis are often associated with flanking repeats.
    PLoS Genet. 2010 May 13;6(5):e1000949 PMID: 20485521
  3. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster.
    Bioessays. 1994 Apr;16(4):269-75 PMID: 8031304
  4. OrthoMCL: identification of ortholog groups for eukaryotic genomes.
    Genome Res. 2003 Sep;13(9):2178-89 PMID: 12952885
  5. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants.
    Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17811-6 PMID: 19815511
  6. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics. 2004 Aug 19;5:113 PMID: 15318951
  7. Eukaryotic genome size databases.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D332-8 PMID: 17090588
  8. LTR_STRUC: a novel search and identification program for LTR retrotransposons.
    Bioinformatics. 2003 Feb 12;19(3):362-7 PMID: 12584121
  9. Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana.
    Genetics. 2004 Nov;168(3):1575-84 PMID: 15579708
  10. Multiple alignment of DNA sequences with MAFFT.
    Methods Mol Biol. 2009;537:39-64 PMID: 19378139
  11. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Nature. 2007 Sep 27;449(7161):463-7 PMID: 17721507
  12. High intrinsic rate of DNA loss in Drosophila.
    Nature. 1996 Nov 28;384(6607):346-9 PMID: 8934517
  13. Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea.
    Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5589-94 PMID: 15064405
  14. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18724-8 PMID: 20921408
  15. Evolutionary rates in partially self-fertilizing species.
    Am Nat. 1992 Jul;140(1):126-48 PMID: 19426068
  16. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62 PMID: 17626786
  17. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss.
    BMC Genomics. 2007 Jul 06;8:218 PMID: 17617907
  18. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis.
    Mol Biol Evol. 2002 Sep;19(9):1407-20 PMID: 12200469
  19. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.
    PLoS One. 2007 Dec 19;2(12):e1326 PMID: 18094749
  20. Mechanisms of recent genome size variation in flowering plants.
    Ann Bot. 2005 Jan;95(1):127-32 PMID: 15596462
  21. The Sorghum bicolor genome and the diversification of grasses.
    Nature. 2009 Jan 29;457(7229):551-6 PMID: 19189423
  22. The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants.
    Plant Physiol. 2008 Nov;148(3):1189-200 PMID: 18775973
  23. Evidence for DNA loss as a determinant of genome size.
    Science. 2000 Feb 11;287(5455):1060-2 PMID: 10669421
  24. The large genome constraint hypothesis: evolution, ecology and phenotype.
    Ann Bot. 2005 Jan;95(1):177-90 PMID: 15596465
  25. Evolution of genome size in Brassicaceae.
    Ann Bot. 2005 Jan;95(1):229-35 PMID: 15596470
  26. The paleontology of intergene retrotransposons of maize.
    Nat Genet. 1998 Sep;20(1):43-5 PMID: 9731528
  27. Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size.
    Plant Biol (Stuttg). 2006 Nov;8(6):770-7 PMID: 17203433
  28. Principles of genome evolution in the Drosophila melanogaster species group.
    PLoS Biol. 2007 Jun;5(6):e152 PMID: 17550304
  29. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.
    Genome Res. 2009 Aug;19(8):1419-28 PMID: 19478138
  30. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.
    PLoS Biol. 2010 Jun 29;8(6):e1000409 PMID: 20613864
  31. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.
    Genome Res. 2006 Oct;16(10):1262-9 PMID: 16963705
  32. The evolution of mammalian gene families.
    PLoS One. 2006 Dec 20;1:e85 PMID: 17183716
  33. Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain.
    Mol Genet Genomics. 2008 Oct;280(4):319-25 PMID: 18677513
  34. Initial sequence of the chimpanzee genome and comparison with the human genome.
    Nature. 2005 Sep 1;437(7055):69-87 PMID: 16136131
  35. The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D1009-14 PMID: 17986450
  36. Genome architecture catalyzes nonrecurrent chromosomal rearrangements.
    Am J Hum Genet. 2003 May;72(5):1101-16 PMID: 12649807
  37. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process.
    Genome Res. 1998 Nov;8(11):1113-30 PMID: 9847076
  38. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
    Genomics. 1991 Nov;11(3):635-50 PMID: 1774068
  39. Building genomic profiles for uncovering segmental homology in the twilight zone.
    Genome Res. 2004 Jun;14(6):1095-106 PMID: 15173115
  40. Evolution of genes and genomes on the Drosophila phylogeny.
    Nature. 2007 Nov 8;450(7167):203-18 PMID: 17994087
  41. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana.
    Science. 2010 Jan 1;327(5961):92-4 PMID: 20044577
  42. Origin and evolution of retroelements based upon their reverse transcriptase sequences.
    EMBO J. 1990 Oct;9(10):3353-62 PMID: 1698615
  43. Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes.
    Genome Res. 2008 Feb;18(2):221-32 PMID: 18083775
  44. The pattern of polymorphism in Arabidopsis thaliana.
    PLoS Biol. 2005 Jul;3(7):e196 PMID: 15907155
  45. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  46. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
    Science. 2006 Sep 15;313(5793):1596-604 PMID: 16973872
  47. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  48. Identification of common molecular subsequences.
    J Mol Biol. 1981 Mar 25;147(1):195-7 PMID: 7265238
  49. An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res. 2002 Apr 1;30(7):1575-84 PMID: 11917018
  50. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
    Science. 2007 Jul 20;317(5836):338-42 PMID: 17641193
  51. Paired-end mapping reveals extensive structural variation in the human genome.
    Science. 2007 Oct 19;318(5849):420-6 PMID: 17901297
  52. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons.
    PLoS One. 2008;3(12):e4047 PMID: 19112500
  53. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.
    Genome Res. 2002 Jul;12(7):1075-9 PMID: 12097344
  54. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana.
    Genome Res. 2005 Apr;15(4):505-15 PMID: 15805492
  55. Whole-genome sequence assembly for mammalian genomes: Arachne 2.
    Genome Res. 2003 Jan;13(1):91-6 PMID: 12529310
  56. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species--Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana.
    Am J Bot. 2005 Apr;92(4):761-7 PMID: 21652456
  57. Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata.
    Plant J. 2006 Dec;48(5):771-83 PMID: 17118036
  58. Selection on major components of angiosperm genomes.
    Science. 2008 Apr 25;320(5875):484-6 PMID: 18436777
  59. A unified classification system for eukaryotic transposable elements.
    Nat Rev Genet. 2007 Dec;8(12):973-82 PMID: 17984973
  60. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  61. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  62. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species.
    Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5224-9 PMID: 16549785
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.807
Published
2011-05-00
Epub
2011-00-10
Pages
476-81
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC3083492
Subset
IM
Grants
NIGMS NIH HHS · R01 GM057994 · United States
NIGMS NIH HHS · R01 GM083068 · United States
NIGMS NIH HHS · R01 GM083068-04 · United States
NIGMS NIH HHS · GM057994 · United States
Databases
GENBANK
ADBK00000000
External Links
PubMed source DOI: 10.1038/ng.807 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2