Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

Plant Physiology

Volumn 151, Issue 1, 2009, Pages 3-15

  Zou, Cheng ^a   Lehti Shiu, Melissa D ^a   Thibaud Nissen, Françoise ^b,c   Prakash, Tanmay ^d   Buell, C Robin ^a   Shiu, Shin Han ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d Novi High School   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA;

ARABIDOPSIS; ARTICLE; EVOLUTION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MULTIGENE FAMILY; PHYSIOLOGY; PLANT GENOME; PSEUDOGENE; RICE;

ARABIDOPSIS; BIOLOGICAL EVOLUTION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MULTIGENE FAMILY; ORYZA SATIVA; PSEUDOGENES;

EID: 70349225934     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.109.140632     Document Type: Article

References (67)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
2. Balakirev ES, Ayala FJ (2003) Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet 37: 123-151
3. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141
4. Benovoy D, Drouin G (2006) Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome. J Mol Evol 62: 511-522
5. Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144
6. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691
7. Brosius J (1991) Retroposons: seeds of evolution. Science 251: 753
8. Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76: 51-74
9. Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36: D959-D965
10. Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, Wahlestedt C, Bajic VB, Kai C, Kawai J, Carninci P, et al (2006) Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet 2: e23
11. Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD (2002) The F-box subunit of the SCF E3 complex is encoded by a diverse super- family of genes in Arabidopsis. Proc Natl Acad Sci USA 99: 11519-11524
12. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80
13. Gingerich DJ, Hanada K, Shiu SH, Vierstra RD (2007) Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell 19: 2329-2348
14. Gray TA, Wilson A, Fortin PJ, Nicholls RD (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc Natl Acad Sci USA 103: 12039-12044
15. Guengerich FP (2004) Cytochrome P450: what have we learned and what are the future issues? Drug Metab Rev 36: 159-197
16. 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
17. Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M (2002) Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 12: 272-280
18. Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M (2005) Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res 33: 2374-2383
19. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, Wynshaw-Boris A, Yoshiki A (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96
20. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci 256: 119-124
21. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800
22. Jacq C, Miller JR, Brownlee GG (1977) A pseudogene structure in 5S DNA of Xenopus laevis. Cell 12: 109-120
23. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303: 1626-1632
24. Kim J, Shiu SH, Thoma S, Li WH, Patterson SE (2006) Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biol 7: R87
25. Korneev SA, Park JH, O'Shea M (1999) Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci 19: 7711-7720
26. Lafontaine I, Fischer G, Talla E, Dujon B (2004) Gene relics in the genome of the yeast Saccharomyces cerevisiae. Gene 335: 1-17
27. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al for the International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
28. Li JT, Zhang Y, Kong L, Liu QR, Wei L (2008) Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res 36: 4833-4844
29. Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, et al (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2: e294
30. Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, et al (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129
31. Li WH (1983) Evolution of duplicate genes and pseudogenes. In M Nei, RK Koehn, eds, Evolution of Genes and Proteins. Sinauer Associates, Sunderland, MA, pp 14-37
32. Li WH, Gojobori T, Nei M (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292: 237-239
33. Little PF (1982) Globin pseudogenes. Cell 28: 683-684
34. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155
35. Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102: 5454-5459
36. McCarrey JR, Riggs AD (1986) Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. Proc Natl Acad Sci USA 83: 679-683
37. Morillo SA, Tax FE (2006) Functional analysis of receptor-like kinases in monocots and dicots. Curr Opin Plant Biol 9: 460-469
38. Mounsey A, Bauer P, Hope IA (2002) Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Genome Res 12: 770-775
39. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562
40. Mudgil Y, Shiu SH, Stone SL, Salt JN, Goring DR (2004) A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiol 134: 59-66
41. Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39: 121-152
42. Nobuta K, Venu RC, Lu C, Beló A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang GL, et al (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25: 473-477
43. Podlaha O, Zhang J (2004) Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol Biol Evol 21: 2202-2209
44. Sakai H, Koyanagi KO, Imanishi T, Itoh T, Gojobori T (2007) Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene 389: 196-203
45. Seoighe C, Gehring C (2004) Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20: 461-464
46. Shiu SH, Bleecker AB (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci USA 98: 10763-10768
47. Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH (2006) Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci USA 103: 2232-2236
48. 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
49. Shiu SH, Shih MC, Li WH (2005) Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol 139: 18-26
50. Thibaud-Nissen F, Ouyang S, Buell CR (2009) Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics 10: 317
51. Tholl D (2006) Terpene synthases and the regulation, diversity and biological roles of terpene metabolism. Curr Opin Plant Biol 9: 297-304
52. Torrents D, Suyama M, Zdobnov E, Bork P (2003) A genome-wide survey of human pseudogenes. Genome Res 13: 2559-2567
53. Vanin EF (1985) Processed pseudogenes: characteristics and evolution. Annu Rev Genet 19: 253-272
54. Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, Zhang G, Liu D, Zhang J, Vang S, et al (2006) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802
55. Wettenhall JM, Smyth GK (2004) limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20: 3705-3706
56. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846
57. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556
58. Yano Y, Saito R, Yoshida N, Yoshiki A, Wynshaw-Boris A, Tomita M, Hirotsune S (2004) A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene. J Mol Med 82: 414-422
59. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38
60. Zhang XH, Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 18: 1241-1250
61. Zhang Y, Wu Y, Liu Y, Han B (2005) Computational identification of 69 retroposons in Arabidopsis. Plant Physiol 138: 935-948
62. Zhang Z, Carriero N, Gerstein M (2004) Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 20: 62-67
63. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22: 1437-1439
64. Zhang Z, Harrison PM, Liu Y, Gerstein M (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13: 2541-2558
65. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, et al (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17: 839-851
66. Zheng D, Gerstein MB (2007) The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet 23: 219-224
67. Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M (2005) Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol 349: 27-45