Dissecting plant genomes with the PLAZA comparative genomics platform

Plant Physiology

Volumn 158, Issue 2, 2012, Pages 590-600

  van Bel, Michiel ^a,b   Proost, Sebastian ^a,b   Wischnitzki, Elisabeth ^a,b   Movahedi, Sara ^a,b   Scheerlinck, Christopher ^c   Van de Peer, Yves ^a,b   Vandepoele, Klaas ^a,b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY COLLEGE GHENT   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; BRYOPHYTA; LILIOPSIDA; VIRIDIPLANTAE;

EID: 84856569514     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.111.189514     Document Type: Article

References (74)

1. Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y (2012) Genome-View: a next-generation genome browser. Nucleic Acids Res (in press)
2. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, et al (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29: 521-527
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, et al (2011) The genome of Theobroma cacao. Nat Genet 43: 101-108
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29
6. Banks JA, Nishiyama T, HasebeM, Bowman JL, GribskovM, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332: 960-963
7. Bennett MD, Leitch IJ (2005) Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann Bot (Lond) 95: 45-90
8. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC (2008) Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 36: e12
9. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, et al (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 28: 951-956
10. Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2: e383
11. Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK, Bohnert HJ, et al (2011) The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 43: 913-918
12. Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, et al (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 103: 11647-11652
13. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797
14. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584
15. Fabry S, Müller K, Lindauer A, Park PB, Cornelius T, Schmitt R (1995) The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes. Curr Genet 28: 333-345
16. Federhen S (2012) The NCBI taxonomy database. Nucleic Acids Res 40: D136-D143
17. Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19: 99-113
18. Fostier J, Proost S, Dhoedt B, Saeys Y, Demeester P, Van de Peer Y, Vandepoele K (2011) A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinformatics 27: 749-756
19. Gabaldón T (2008) Large-scale assignment of orthology: back to phylogenetics? Genome Biol 9: 235
20. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638
21. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: D1178-D1186
22. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704
23. Hahn MW (2007) Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol 8: R141
24. Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148: 993-1003
25. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43: 476-481
26. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-D215
27. Hurst LD, Pá l C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310
28. Huynen MA, Bork P (1998) Measuring genome evolution. Proc Natl Acad Sci USA 95: 5849-5856
29. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768
30. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
31. Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P (2008) eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res 36: D250-D254
32. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, et al (2010) Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 38: D563-D569
33. Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338
34. Koonin EV (2009) Evolution of genome architecture. Int J Biochem Cell Biol 41: 298-306
35. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645
36. Kuzniar A, van Ham RC, Pongor S, Leunissen JA (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 24: 539-551
37. Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189
38. Linard B, Thompson JD, Poch O, Lecompte O (2011) OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics 12: 11
39. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536
40. Lyons E, Pedersen B, Kane J, AlamM, Ming R, TangH, Wang X, Bowers J, Paterson A, Lisch D, et al (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148: 1772-1781
41. Martinez DA, Nelson MA (2010) The next generation becomes the now generation. PLoS Genet 6: e1000906
42. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250
43. Meyer IM, Durbin R (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res 32: 776-783
44. Michalak P (2008) Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91: 243-248
45. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996
46. Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA 107: 4623-4628
47. Movahedi S, Van de Peer Y, Vandepoele K (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol 156: 1316-1330
48. Osbourn A (2010) Gene clusters for secondary metabolic pathways: an emerging theme in plant biology. Plant Physiol 154: 531-535
49. Osbourn AE, Field B (2009) Operons. Cell Mol Life Sci 66: 3755-3775
50. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, et al (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887
51. Page RD, Charleston MA (1997) From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol 7: 231-240
52. Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, et al (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104: 7705-7710
53. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556
54. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, et al (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329: 223-226
55. Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K (2012) i-ADHoRe 3.0: fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res (in press)
56. Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21: 3718-3731
57. Pryszcz LP, Huerta-Cepas J, Gabaldón T (2011) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res 39: e32
58. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69
59. RouardM, Guignon V, AluomeC, LaporteMA, Droc G, WaldeC, Zmasek CM, Périn C, Conte MG (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 39: D1095-D1102
60. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15: 227-239
61. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
62. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115
63. Schuster SC (2008) Next-generation sequencing transforms today's biology. Nat Methods 5: 16-18
64. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43: 109-116
65. Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P (2011) Orthology prediction methods: a quality assessment using curated protein families. Bioessays 33: 769-780
66. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604
67. Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K (2009) The flowering world: a tale of duplications. Trends Plant Sci 14: 680-688
68. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, et al (2010) The genome of the domesticated apple (Malus 3 domestica Borkh.). Nat Genet 42: 833-839
69. Vernot B, Stolzer M, Goldman A, Durand D (2008) Reconciliation with non-binary species trees. J Comput Biol 15: 981-1006
70. Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, et al (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324: 268-272
71. Yi G, Sze SH, Thon MR (2007) Identifying clusters of functionally related genes in genomes. Bioinformatics 23: 1053-1060
72. Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520-524
73. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92
74. Zmasek CM, Eddy SR (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828