Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 627-640

  Lai, Alvina G ^a   Denton Giles, Matthew ^a   Mueller Roeber, Bernd ^b,c   Schippers, Jos H M ^b,c   Dijkwel, Paul P ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b UNIVERSITY OF POTSDAM   (Germany)

^c MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Allelic variants; Comparative genomics; Drafted genomes; Genome partitioning; Haplotype

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS; ARTICLE; GENE LOCUS; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; HOMOZYGOTE; INDEL MUTATION; PLANT GENOME;

ARABIDOPSIS; GENETIC LOCI; GENOME, PLANT; GENOMIC STRUCTURAL VARIATION; HAPLOTYPES; HOMOZYGOTE; INDEL MUTATION;

EID: 84856400714     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr038     Document Type: Article

References (94)

1. Akama T, et al. 2009. Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions. J Bacteriol. 191:3321-3327.
2. Al-Shahrour F, et al. 2010. Selection upon genome architecture: conservation of functional neighborhoods with changing genes. PLoS Comput Biol. 6:e1000953. doi:1000910.1001371/journal.pcbi.1000953
3. Alcázar R, Garcia AV, Parker JE, Reymond M. 2009. Incremental steps toward incompatibility revealed by Arabidopsis epistatic interactions modulating salicylic acid pathway activation. Proc Natl Acad Sci U S A. 106:334-339.
4. Alcázar R, et al. 2010. Natural variation at Strubbelig Receptor Kinase 3 drives immune-triggered incompatibilities between Arabidopsis thaliana accessions. Nat Genet. 42:1135-1139.
5. Alonso-Blanco C, et al. 2009. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell. 21:1877-1896.
6. Altshuler DL, et al. 2010. A map of human genome variation from population-scale sequencing. Nature. 467:1061-1073.
7. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. 2001. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11:1005-1017. (Pubitemid 32834546)
8. Bennetzen JL. 2005. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev. 15:621-627. (Pubitemid 41532335)
9. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456:53-59.
10. Bikard D, et al. 2009. Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science. 323:623-626.
11. Birtle Z, Goodstadt L, Ponting C. 2005. Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics. 6:120.
12. Blewitt ME, et al. 2005. An N-ethyl-N-nitrosourea screen for genes involved in variegation in the mouse. Proc Natl Acad Sci U S A. 102:7629-7634. (Pubitemid 40741022)
13. Bowman JL, Floyd SK, Sakakibara K. 2007. Green genes-comparative genomics of the green branch of life. Cell. 129:229-234. (Pubitemid 46574980)
14. Butler J, et al. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18:810-820. (Pubitemid 351645071)
15. Cai JJ, Macpherson JM, Sella G, Petrov DA. 2009. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 5:e1000336. doi:1000310.1001371/journal.pgen.1000336
16. Chain PSG, et al. 2009. Genome project standards in a new era of sequencing. Science. 326:236-237.
17. Chen K, et al. 2009. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 6:677-681.
18. Choi JH, et al. 2008. A machine-learning approach to combined evidence validation of genome assemblies. Bioinformatics. 24:744-750.
19. Collins FS, Morgan M, Patrinos A. 2003. The human genome project: lessons from large-scale biology. Science. 300:286-290. (Pubitemid 36433711)
20. Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 10:691-703.
21. Darling A, Mau B, Perna N. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 5:e11147. doi:11110.11371/journal.pone.0011147
22. Drummond A, et al. 2010. Geneious v5.1. [cited 2011 Feb]. Available from: http://www.geneious.com/.
23. Ellegren H. 2008. Comparative genomics and the study of evolution by natural selection. Mol Ecol. 17:4586-4596.
24. Emes RD, Goodstadt L, Winter EE, Ponting CP. 2003. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet. 12:701-709. (Pubitemid 36416957)
25. Erlich Y, et al. 2009. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res. 19:1243-1253.
26. Feuillet C, Keller B. 2002. Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot. 89:3-10. (Pubitemid 34527376)
27. Feuk L, Carson AR, Scherer SW. 2006. Structural variation in the human genome. Nat Rev Genet. 7:85-97. (Pubitemid 43128895)
28. Fransz PF, et al. 2000. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell. 100:367-376. (Pubitemid 30353092)
29. Frazer KA, Murray SS, Schork NJ, Topol EJ. 2009. Human genetic variation and its contribution to complex traits. Nat Rev Genet. 10:241-251.
30. Fujiyama A, et al. 2002. Construction and analysis of a human-chimpanzee comparative clone map. Science. 295:131-134. (Pubitemid 34052362)
31. Gresham D, Dunham MJ, Botstein D. 2008. Comparing whole genomes using DNA microarrays. Nat Rev Genet. 9:291-302. (Pubitemid 351399834)
32. He L, Dooner HK. 2009. Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc Natl Acad Sci U S A. 106:8410-8416.
33. Heard E, et al. 2010. Ten years of genetics and genomics: what have we achieved and where are we heading? Nat Rev Genet. 11:723-733.
34. Heuer S, et al. 2009. Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure. Plant Biotechnol J. 7:456-471.
35. Hirotsune S, et al. 2003. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature. 423:91-96. (Pubitemid 36569588)
36. Hoberman R, et al. 2009. A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res. 19:1542-1552.
37. Hollister JD, et al. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A. 108:2322-2327.
38. Hurwitz BL, et al. 2010. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63:990-1003.
39. Johnson ME, et al. 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature. 413:514-519. (Pubitemid 32938748)
40. Johnson ME, et al. 2006. Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A. 103:17626-17631. (Pubitemid 44852211)
41. Kidd JM, et al. 2008. Mapping and sequencing of structural variation from eight human genomes. Nature. 453:56-64. (Pubitemid 351630326)
42. Kidd JM, et al. 2010. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods. 7:365-371.
43. Koonin EV. 2009. Darwinian evolution in the light of genomics. Nucleic Acids Res. 37:1011-1034.
44. Koornneef M, Alonso-Blanco C, Vreugdenhil D. 2004. Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol. 55:141-172. (Pubitemid 38940929)
45. Korbel JO, et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science. 318:420-426. (Pubitemid 47614521)
46. Krawitz P, et al. 2010. Microindel detection in short-read sequence data. Bioinformatics 26:722-729.
47. Kuhl H, et al. 2010. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics. 11:68.
48. Larkin DM, et al. 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res. 19:770-777.
49. Lewin HA, Larkin DM, Pontius J, O'Brien SJ. 2009. Every genome sequence needs a good map. Genome Res. 19:1925-1928.
50. Lippman Z, et al. 2004. Role of transposable elements in heterochro-matin and epigenetic control. Nature. 430:471-476. (Pubitemid 38987911)
51. Lisch D. 2009. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol. 60:43-66.
52. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science. 290:1151.
53. Marques-Bonet T, Ryder OA, Eichler EE. 2009. Sequencing primate genomes: what have we learned? Annu Rev Genomics Hum Genet. 10:355-386.
54. Martinez Barrio A, et al. 2009. Targeted resequencing and analysis of the diamond-blackfan anemia disease locus RPS19. PLoS One. 4:e6172. doi:6110.1371/journal.pone.0006172
55. McKernan KJ, et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19:1527-1541.
56. Meader S, Hillier LW, Locke D, Ponting CP, Lunter G. 2010. Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res. 20:675-684.
57. Meyers BC, Kaushik S, Nandety RS. 2005. Evolving disease resistance genes. Curr Opin Plant Biol. 8:129-134. (Pubitemid 40323540)
58. Michaels SD, He Y, Scortecci KC, Amasino RM. 2003. Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc Natl Acad Sci U S A. 100:10102-10107. (Pubitemid 37087074)
59. Nishiyama T, et al. 2003. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A. 100:8007-8012. (Pubitemid 36760085)
60. Ossowski S, et al. 2008. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 18:2024-2033.
61. Perry GH, et al. 2008. Copy number variation and evolution in humans and chimpanzees. Genome Res. 18:1698-1710.
62. Pool JE, Hellmann I, Jensen JD, Nielsen R. 2010. Population genetic inference from genomic sequence variation. Genome Res. 20:291-300.
63. Rieseberg LH, Whitton J, Gardner K. 1999. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics. 152:713-727. (Pubitemid 29272722)
64. Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 132:365-386.
65. Samonte RV, Eichler EE. 2002. Segmental duplications and the evolution of the primate genome. Nat Rev Genet. 3:65-72. (Pubitemid 34506605)
66. Santuari L, Hardtke CS. 2010. The case for resequencing studies of Arabidopsis thaliana accessions: mining the dark matter of natural genetic variation. F1000 Biol Rep. 2:85. doi: 10.3410/B2-85.
67. Santuari L, et al. 2010. Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol. 11:R4.
68. Schatz MC, Delcher AL, Salzberg SL. 2010. Assembly of large genomes using second-generation sequencing. Genome Res. 20:1165-1173.
69. Schmuths H, Meister A, Horres R, Bachmann K. 2004. Genome size variation among accessions of Arabidopsis thaliana. Ann Bot. 93:317-321. (Pubitemid 41295625)
70. Sebat J, et al. 2004. Large-scale copy number polymorphism in the human genome. Science. 305:525-528. (Pubitemid 38971344)
71. Sharp AJ, Cheng Z, Eichler EE. 2006. Structural variation of the human genome. Annu Rev Genomics Hum Genet. 7:407-442. (Pubitemid 44641878)
72. Shen YF, et al. 2010. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 20:273-280.
73. Simpson JT, et al. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-1123.
74. Snyder M, Du J, Gerstein M. 2010. Personal genome sequencing: current approaches and challenges. Genes Dev. 24:423-431.
75. Stanke M, Morgenstern B. 2005. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33:W465-W467. (Pubitemid 44529963)
76. Sureshkumar S, et al. 2009. A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science. 323:1060-1063.
77. Tsai IJ, Otto TD, Berriman M. 2010. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 11:R41. doi:10.1186/gb-2010-1111-1184-r1141
78. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet. 42:260-263.
79. Tuzun E, et al. 2005. Fine-scale structural variation of the human genome. Nat Genet. 37:727-732. (Pubitemid 41754889)
80. van der Biezen EA, Brandwagt BF, van Leeuwen W, Nijkamp HJJ, Hille J. 1996. Identification and isolation of the FEEBLY gene from tomato by transposon tagging. Mol Gen Genet. 251:267-280.
81. Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500-501. (Pubitemid 46323134)
82. Weigel D, Mott R. 2009. The 1001 Genomes Project for Arabidopsis thaliana. Genome Biol. 10:107. doi:110.1186/gb-2009-1110-1185-1107
83. Weil C, Martienssen R. 2008. Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev. 18:188-192. (Pubitemid 351749827)
84. Wheelan SJ, Aizawa Y, Han JS, Boeke JD. 2005. Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Res. 15:1073-1078. (Pubitemid 41126862)
85. White MJD. 1978. Chain processes in chromosomal speciation. Syst Biol. 27:285-298.
86. Wood HM, et al. 2010. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nano-gram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res. 38:e151. doi:110.1093/nar/gkq1510.
87. Young AL, et al. 2010. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res. 20:249-256.
88. Zeller G, et al. 2008. Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res. 18:918-929. (Pubitemid 351793064)
89. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. (Pubitemid 351645072)
90. Zhang F, Gu W, Hurles ME, Lupski JR. 2009. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 10:451-481.
91. Zhang J. 2003. Evolution by gene duplication: an update. Trends Ecol Evol. 18:292-298. (Pubitemid 36631749)
92. Zhao S, et al. 2004. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res. 14:1851-1860. (Pubitemid 39386498)
93. Zimmerli L, et al. 2008. The xenobiotic B-aminobutyric acid enhances Arabidopsis thermotolerance. Plant J. 53:144-156. (Pubitemid 350265250)
94. Ziolkowski PA, Koczyk G, Galganski L, Sadowski J. 2009. Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res. 37:3189-3201.