Gene order in plants: A slow but sure shuffle

New Phytologist

Volumn 168, Issue 1, 2005, Pages 51-60

  Vision, Todd J ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Comparative mapping; Gene duplication; Gene loss; Gene order; Synteny

Indexed keywords

EVOLUTION; GENE EXPRESSION; GENOMICS; MAPPING METHOD; PLANT; POLYMORPHISM;

CHROMOSOME MAP; EVOLUTION; GENE; GENE DUPLICATION; GENETIC POLYMORPHISM; GENETICS; PLANT; PLANT CHROMOSOME; REVIEW;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; EVOLUTION; GENE DUPLICATION; GENES, PLANT; PLANTS; POLYMORPHISM, GENETIC;

EID: 32944469216     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2005.01537.x     Document Type: Review

References (69)

1. Akhunov ED Akhunova AR Linkiewicz AM Dubcovsky J Hummel D Lazo G Chao S Anderson OD David J Qi L Echalier B Gill BS Miftahudin Gustafson JP La Rota M Sorrells ME Zhang D Nguyen HT Kalavacharla V Hossain K Kianian SF Peng J Lapitan NL Wennerlind EJ Nduati V Anderson JA Sidhu D Gill KS McGuire PE Qualset CO Dvorak J. 2003a. Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates. Proceedings of the National Academy of Sciences, USA 100 : 10836 10841.
2. Akhunov ED Goodyear AW Geng S Qi LL Echalier B Gill BS Miftahudin Gustafson JP Lazo G Chao S Anderson OD Linkiewicz AM Dubcovsky J La Rota M Sorrells ME Zhang D Nguyen HT Kalavacharla V Hossain K Kianian SF Peng J Lapitan NL Gonzalez-Hernandez JL Anderson JA Choi DW Close TJ Dilbirligi M Gill KS Walker-Simmons MK Steber C McGuire PE Qualset CO Dvorak J. 2003b. The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Research 13 : 753 763.
3. Allen KD. 2002. Assaying gene content in Arabidopsis. Proceedings of the National Academy of Sciences, USA 99 : 9568 9572.
4. Aoki S. 2004. Resurrection of an ancestral gene: functional and evolutionary analyses of the Ngrol genes transferred from Agrobacterium to Nicotiana. Journal of Plant Research 117 : 329 337.
5. Bennetzen JL Coleman C Liu R Ma J Ramakrishna W. 2004. Consistent over-estimation of gene number in complex plant genomes. Current Opinions in Plant Biology 7 : 732 736.
6. Bennetzen JL Ma J Devos KM. 2005. Mechanisms of recent genome size variation in flowering plants. Annals of Botany (London) 95 : 127 132.
7. Blanc G Hokamp K Wolfe KH. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research 13 : 137 144.
8. Blanc G Wolfe KH. 2004a. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16 : 1679 1691.
9. Blanc G Wolfe KH. 2004b. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16 : 1667 1678.
10. Bowers JE Chapman BA Rong J Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 : 433 438.
11. Brunner S Fengler K Morgante M Tingey S Rafalski A. 2005. Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17 : 343 360.
12. Calabrese PP Chakravarty S Vision TJ. 2003. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19 : i74-80.
13. Cannon SB Mitra A Andrew B Young ND May G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology 4 : 10.
14. Charlesworth D. 2002. Plant sex determination and sex chromosomes. Heredity 88 : 94 101.
15. Conant GC Wagner A. 2005. The rarity of gene shuffling in conserved genes. Genome Biology 6 : R50.
16. Doganlar S Frary A Daunay MC Lester RN Tanksley SD. 2002. A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the solanaceae. Genetics 161 : 1697 1711.
17. Domazet-Loso T Tautz D. 2003. An evolutionary analysis of orphan genes in Drosophila. Genome Research 13 : 2213 2219.
18. Durbin ML McCaig B Clegg MT. 2000. Molecular evolution of the chalcone synthase multigene family in the morning glory genome. Plant Molecular Biology 42 : 79 92.
19. Dvorak J Yang ZL You FM Luo MC. 2004. Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics 168 : 1665 1675.
20. Eichler EE Sankoff D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301 : 793 797.
21. Fu H Dooner HK. 2002. Intraspecific violation of genetic colinearity and its implications in maize. Proceedings of the National Academy of Sciences, USA 99 : 9573 9578.
22. Gale MD Devos KM. 1998. Comparative genetics in the grasses. Proceedings of the National Academy of Sciences, USA 95 : 1971 1974.
23. Gaut BS. 2002. Evolutionary dynamics of the grasses. New Phytologist 154 : 15 28.
24. Goff SA Ricke D Lan TH Presting G Wang R Dunn M Glazebrook J Sessions A Oeller P Varma H Hadley D Hutchison D Martin C Katagiri F Lange BM Moughamer T Xia Y Budworth P Zhong J Miguel T Paszkowski U Zhang S Colbert M Sun WL Chen L Cooper B Park S Wood TC Mao L Quail P Wing R Dean R Yu Y Zharkikh A Shen R Sahasrabudhe S Thomas A Cannings R Gutin A Pruss D Reid J Tavtigian S Mitchell J Eldredge G Scholl T Miller RM Bhatnagar S Adey N Rubano T Tusneem N Robinson R Feldhaus J Macalma T Oliphant A Briggs S. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296 : 92 100.
25. Gordo I Charlesworth B. 2001. Genetic linkage and molecular evolution. Current Biology 11 : R684 R686.
26. Graham MA Silverstein KA Cannon SB VandenBosch KA. 2004. Computational identification and characterization of novel genes from legumes. Plant Physiology 135 : 1179 1197.
27. Hampson SE Gaut BS Baldi P. 2005. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21 : 1339 1348.
28. Huan J Prins J Wang W Vision TJ. 2003. Reconstruction of ancestral gene order following segmental duplication and gene loss. Proceedings of the 2nd IEEE Computational Systems Bioinformatics Conference (CSB 2003) 484 485. http://csdl2.computer.org/comp/proceedings/csb/2003/2000/00/20000484.pdf
29. Jiang N Bao Z Zhang X Eddy SR Wessler SR. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431 : 569 573.
30. Kashkush K Feldman MW Levy A. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160.
31. Katju V Lynch M. 2003. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 165 : 1793 1803.
32. Kellogg EA Bennetzen JL. 2004. The evolution of nuclear genome structure in seed plants. American Journal of Botany 91 : 1709 1725.
33. Ku HM Vision T Liu J Tanksley SD. 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of Sciences, USA 97 : 9121 9126.
34. Ku HM Liu J Doganlar S Tanksley SD. 2001. Exploitation of Arabidopsis-tomato synteny to construct a high-resolution map of the ovate containing region in tomato chromosome 2. Genome 44 : 470 475.
35. Kusaba M Dwyer K Hendershot J Vrebalov J Nasrallah JB Nasrallah ME. 2001. Self-incompatibility in the genus Arabidopsis: characterization of the S locus in the outcrossing A. lyrata and its autogamous relative A. thaliana. Plant Cell 13 : 627 643.
36. Langham RJ Walsh J Dunn M Ko C Goff SA Freeling M. 2004. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166 : 935 945.
37. Lee JM Sonnhammer EL. 2003. Genomic clustering analysis of pathways in eukaryotes. Genome Research 13 : 875 882.
38. Levin DA. 2002. The role of chromosomal change in plant evolution. Oxford, UK : Oxford University Press.
39. Livingstone KD Lackney VK Blauth JR van Wijk R Jahn MK. 1999. Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152 : 1183 1202.
40. Lockton S Gaut BS. 2005. Plant conserved non-coding sequences and paralogue evolution. Trend in Genetics 21 : 60 65.
41. Long M Deutsch M Wang W Betran E Brunet FG Zhang J. 2003. Origin of new genes: evidence from experimental and computational analyses. Genetica 18 : 171 182.
42. Lynch M Conery J. 2001. The evolutionary fate and consequences of duplicate genes. Science 290 : 1151 1155.
43. Lynch M Conery JS. 2003. The evolutionary demography of duplicate genes. Journal of Structural and Functional Genomics 3 : 35 44.
44. Maere S De Bodt S Raes J Casneuf T van Montagu M Kuiper M van de Peer Y. 2005. Modeling gene and genome duplication in the eukaryotes. Proceedings of the National Academy of Sciences, USA 102 : 5454 5459.
45. Mayer K Murphy G Tarchini R Wambutt R Volckaert G Pohl T Dusterhoft A Stiekema W Entian KD Terryn N Lemcke K Haase D Hall CR van Dodeweerd AM Tingey SV Mewes HW Bevan MW Bancroft I. 2001. Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Research 11 : 1167 1174.
46. Moore RC Purugganan MD. 2003. The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences, USA 100 : 15682 15687.
47. Nadeau JH Sankoff D. 1998. Counting on comparative maps. Trends in Genetics 14 : 495 501.
48. Paterson AH Bowers JE Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, USA 101 : 9903 9908.
49. Remington DL Vision TJ Guilfolye TJ Reed JA. 2004. Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiology 135 : 1738 1752.
50. Rudd S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8 : 321 329.
51. Sankoff D. 1999. Genome rearrangement with gene families. Bioinformatics 15 : 909 917.
52. Scherrer B Isidore E Klein P Kim JS Bellec A Chalhoub B Keller B Feuillet C. 2005. Large intraspecific haplotype variability at the rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17 : 361 374.
53. Seoighe C Gehring C. 2004. Genome duplication led to a highly selective expansion of the Arabidopsis thaliana proteome. Trends in Genetics 20 : 461 464.
54. Seoighe C Federspiel N Jones T Hansen N Bivolarovic V Surzycki R Tamse R Komp C Huizar L Davis RW Scherer S Tait E Shaw DJ Harris D Murphy L Oliver K Taylor K Rajandream MA Barrell BG Wolfe KH. 2000. Prevalence of small inversions in yeast gene order evolution. Proceedings of the National Academy of Sciences, USA 97 : 14433 14437.
55. Shiu SH Karlowski WM Pan R Tzeng YH Mayer KF Li WH. 2004. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16 : 1220 1234.
56. Simillion C Vandepoele K van Montagu MC Zabeau M Van de Peer Y. 2002. The hidden duplication past of Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 99 : 13627 13632.
57. Simillion C Vandepoele K Saeys Y van de Peer Y. 2004. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Research 14 : 1095 1106.
58. Simmonds NW. 1976. Evolution of crop plants. London, UK : Longman.
59. Singer GA Lloyd AT Huminiecki LB Wolfe KH. 2005. Clusters of coexpressed genes in mammalian genomes are conserved by natural selection. Molecular Biology and Evolution 22 : 767 775.
60. Song R Messing J. 2003. Gene expression of a gene family in maize based on noncollinear haplotypes. Proceedings of the National Academy of Sciences, USA 100 : 9055 9060.
61. Stracke S Kistner C Yoshida S Mulder L Sato S Kaneko T Tabata S Sandal N Stougaard J Szczyglowski K Parniske M. 2002. A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417 : 959 962.
62. Tian D Araki H Stahl E Bergelson J Kreitman M. 2002. Signature of balancing selection in Arabidopsis. Proceedings of the National Academy of Sciences, USA 99 : 11525 11530.
63. Vandepoele K Simillion C Van de Peer Y. 2002. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends in Genetics 18 : 606 608.
64. Vision TJ Brown DG Tanksley SD. 2000. The origins of genomic duplications in Arabidopsis. Science 290 : 2114 2117.
65. Wang X Shi X Hao B Ge S Luo J. 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytologist 165 : 937 946.
66. Wendel JF Cronn RC Johnston JS Price HJ. 2002. Feast and famine in plant genomes. Genetica 115 : 37 47.
67. Williams EJ Bowles DJ. 2004. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Research 14 : 1060 1067.
68. Yu J Hu S Wang J Wong GK Li S Liu B Deng Y Dai L Zhou Y Zhang X Cao M Liu J Sun J Tang J Chen Y Huang X Lin W Ye C Tong W Cong L Geng J Han Y Li L Li W Hu G Li J Liu Z Qi Q Li T Wang X Lu H Wu T Zhu M Ni P Han H Dong W Ren X Feng X Cui P Li X Wang H Xu X Zhai W Xu Z Zhang J He S Xu J Zhang K Zheng X Dong J Zeng W Tao L Ye J Tan J Chen X He J Liu D Tian W Tian C Xia H Bao Q Li G Gao H Cao T Zhao W Li P Chen W Zhang Y Hu J Liu S Yang J Zhang G Xiong Y Li Z Mao L Zhou C Zhu Z Chen R Hao B Zheng W Chen S Guo W Tao M Zhu L Yuan L Yang H. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 : 79 92.
69. Ziolkowski PA Blanc G Sadowski J. 2003. Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome. Nucleic Acids Research 31 : 1339 1350.