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

Nature Genetics

Volumn 43, Issue 5, 2011, Pages 476-483

  Hu, Tina T ^a,m,n   Pattyn, Pedro ^b,c   Bakker, Erica G ^d,e,m,o   Cao, Jun ^f   Cheng, Jan Fang ^g   Clark, Richard M ^f,m,p   Fahlgren, Noah ^e   Fawcett, Jeffrey A ^b,c,m,q   Grimwood, Jane ^g,h   Gundlach, Heidrun ⁱ   Haberer, Georg ⁱ   Hollister, Jesse D ^j,m,r   Ossowski, Stephan ^f,m,s   Ottilar, Robert P ^g   Salamov, Asaf A ^g   Schneeberger, Korbinian ^f,m   Spannagl, Manuel ⁱ   Wang, Xi ^i,m   Yang, Liang ^j   Nasrallah, Mikhail E ^k   Bergelson, Joy ^d   Carrington, James C ^e   Gaut, Brandon S ^j   Schmutz, Jeremy ^g,h   Mayer, Klaus F X ⁱ   Van De Peer, Yves ^b,c   Grigoriev, Igor V ^g   Nordborg, Magnus ^a,l   Weigel, Detlef ^f   Guo, Ya Long ^f   more..

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

^d UNIVERSITY OF CHICAGO   (United States)

^e OREGON STATE UNIVERSITY   (United States)

^f MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^g DOE JOINT GENOME INSTITUTE   (United States)

^h HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

ⁱ INSTITUTE OF EPIDEMIOLOGY   (Germany)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k Department of Obstetrics Gynecology   (United States)

^l GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

^m PRINCETON UNIVERSITY   (United States)

ⁿ DOW AGROSCIENCES LLC   (United States)

^o UNIVERSITY OF UTAH   (United States)

^p GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^q HARVARD UNIVERSITY   (United States)

^r CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^s MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; GENE DELETION; GENE INSERTION; GENE REARRANGEMENT; GENE SEQUENCE; GENOME SIZE; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; TRANSPOSON;

ARABIDOPSIS; BASE SEQUENCE; CENTROMERE; CHROMOSOMES, PLANT; DNA, PLANT; EVOLUTION, MOLECULAR; GENOME, PLANT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

ARABIDOPSIS; ARABIDOPSIS LYRATA; ARABIDOPSIS THALIANA;

EID: 79955468851     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.807     Document Type: Article

References (65)

1. Greilhuber, J. et al. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol. 8, 770-777 (2006). (Pubitemid 46092475)
2. Gregory, T.R. et al. Eukaryotic genome size databases. Nucleic Acids Res. 35, D332-D338 (2007). (Pubitemid 46056226)
3. Gaut, B.S. & Ross-Ibarra, J. Selection on major components of angiosperm genomes. Science 320, 484-486 (2008). (Pubitemid 351590630)
4. Pellicer, J., Fay, M.F. & Leitch, I.J. The largest eukaryotic genome of them all? Bot. J. Linn. Soc. 164, 10-15 (2010).
5. Bennetzen, J.L., Ma, J. & Devos, K.M. Mechanisms of recent genome size variation in fowering plants. Ann. Bot. 95, 127-132 (2005). (Pubitemid 41214455)
6. Hawkins, J.S., Proulx, S.R., Rapp, R.A. & Wendel, J.F. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc. Natl. Acad. Sci. USA 106, 17811-17816 (2009).
7. Piegu, B. et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16, 1262-1269 (2006). (Pubitemid 44506959)
8. Vitte, C., Panaud, O. & Quesneville, H. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifcations followed by rapid DNA loss. BMC Genomics 8, 218 (2007).
9. Woodhouse, M.R. et al. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8, e1000409 (2010).
10. Paterson, A.H. et al. The Sorghum bicolor genome and the diversifcation of grasses. Nature 457, 551-556 (2009).
11. Johnston, J.S. et al. Evolution of genome size in Brassicaceae. Ann. Bot. 95, 229-235 (2005). (Pubitemid 41214463)
12. Oyama, R.K. et al. The shrunken genome of Arabidopsis thaliana. Plant Syst. Evol. 273, 257-271 (2008).
13. Wright, S.I., Lauga, B. & Charlesworth, D. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol. Biol. Evol. 19, 1407-1420 (2002). (Pubitemid 36752766)
14. Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92-94 (2010).
15. Beilstein, M.A., Nagalingum, N.S., Clements, M.D., Manchester, S.R. & Mathews, S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 107, 18724-18728 (2010).
16. Kuittinen, H. et al. Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168, 1575-1584 (2004). (Pubitemid 40007370)
17. Koch, M.A. & Kiefer, M. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diplod species\Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana. Am. J. Bot 92, 761-767 (2005). (Pubitemid 40452085)
18. Yogeeswaran, K. et al. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15, 505-515 (2005). (Pubitemid 41057814)
19. Lysak, M.A. et al. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl. Acad. Sci. USA 103, 5224-5229 (2006).
20. Berr, A. et al. Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata. Plant J. 48, 771-783 (2006). (Pubitemid 44748255)
21. Swarbreck, D. et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36, D1009-10014 (2007).
22. Lim, J.K. & Simmons, M.J. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16, 269-275 (1994). (Pubitemid 2073509)
23. Stankiewicz, P. et al. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am. J. Hum. Genet. 72, 1101-1116 (2003). (Pubitemid 36529999)
24. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007). (Pubitemid 47614521)
25. Lee, J., Han, K., Meyer, T.J., Kim, H.S. & Batzer, M.A. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS ONE 3, e4047 (2008).
26. Braumann, I., van den Berg, M.A. & Kempken, F. Strain-specifc retrotransposon-mediated recombination in commercially used Aspergillus niger strain. Mol. Genet. Genomics 280, 319-325 (2008).
27. Woodhouse, M.R., Pedersen, B. & Freeling, M. Transposed genes in Arabidopsis are often associated with fanking repeats. PLoS Genet. 6, e1000949 (2010).
28. Ranz, J.M. et al. Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol. 5, e152 (2007).
29. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).
30. Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338-342 (2007). (Pubitemid 47106367)
31. Borevitz, J.O. et al. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl. Acad. Sci. USA 104, 12057-12062 (2007). (Pubitemid 47185629)
32. Enright, A.J., Van Dongen, S. & Ouzounis, C.A. An effcient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584 (2002). (Pubitemid 34679732)
33. Michelmore, R.W. & Meyers, B.C. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8, 1113-1130 (1998). (Pubitemid 29027217)
34. Thomas, J.H. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res. 16, 1017-1030 (2006). (Pubitemid 44162261)
35. Yang, X. et al. The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. Plant Physiol. 148, 1189-1200 (2008). (Pubitemid 352847485)
36. Tuskan, G.A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604 (2006). (Pubitemid 44414027)
37. Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467 (2007). (Pubitemid 47509545)
38. Velasco, R. et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2, e1326 (2007).
39. Li, L., Stoeckert, C.J. Jr. & Roos, D.S. OrthoMCL: identifcation of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003). (Pubitemid 37161775)
40. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y. & Bennetzen, J.L. The paleontology of intergene retrotransposons of maize. Nat Genet. 20, 43-45 (1998). (Pubitemid 28410341)
41. Devos, K.M., Brown, J.K. & Bennetzen, J.L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075-1079 (2002). (Pubitemid 34785200)
42. Hollister, J.D. & Gaut, B.S. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19, 1419-1428 (2009).
43. Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005).
44. Petrov, D.A., Sangster, T.A., Johnston, J.S., Hartl, D.L. & Shaw, K.L. Evidence for DNA loss as a determinant of genome size. Science 287, 1060-1062 (2000). (Pubitemid 30094365)
45. Petrov, D.A., Lozovskaya, E.R. & Hartl, D.L. High intrinsic rate of DNA loss in Drosophila. Nature 384, 346-349 (1996). (Pubitemid 26408513)
46. Charlesworth, B. Evolutionary rates in partially self-fertilizing species. Am. Nat 140, 126-148 (1992).
47. Knight, C.A., Molinari, N.A. & Petrov, D.A. The large genome constraint hypothesis: evolution, ecology and phenotype. Ann. Bot. 95, 177-190 (2005). (Pubitemid 41214458)
48. Jaffe, D.B. et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91-96 (2003).
49. Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N. & Hahn, M.W. The evolution of mammalian gene families. PLoS ONE 1, e85 (2006).
50. Prachumwat, A. & Li, W.H. Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Res. 18, 221-232 (2008) (Pubitemid 351240732)
51. Drosophila 12 Genomes Consortium. et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007).
52. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. The CLUSTAL-X Windows interface: fexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 (1997). (Pubitemid 28022245)
53. Wicker, T. et al. A unifed classifcation system for eukaryotic transposable elements. Nat Rev. Genet. 8, 973-982 (2007). (Pubitemid 350129169)
54. McCarthy, E.M. & McDonald, J.F. LTR-STRUC: a novel search and identifcation program for LTR retrotransposons. Bioinformatics 19, 362-367 (2003).
55. Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
56. Xiong, Y. & Eickbush, T.H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9, 3353-3362 (1990).
57. Zhang, X. & Wessler, S.R. Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc. Natl. Acad. Sci. USA 101, 5589-5594 (2004). (Pubitemid 38481200)
58. Swofford, D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods): Version 4. (Sinauer Associates, Sunderland, Massachusetts, USA, 2003).
59. Simillion, C., Vandepoele, K., Saeys, Y. & Van de Peer, Y. Building genomic profles for uncovering segmental homology in the twilight zone. Genome Res. 14, 1095-1106 (2004). (Pubitemid 38811546)
60. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997). (Pubitemid 27359211)
61. Smith, T.F. & Waterman, M.S. Identifcation of common molecular subsequences. J. Mol. Biol. 147, 195-197 (1981).
62. Pearson, W.R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635-650 (1991).
63. Kent, W.J. BLAT\the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
64. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
65. Katoh, K., Asimenos, G. & Toh, H. Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol. 537, 39-64 (2009).