Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 1357-1368

  Sakai, Hiroaki ^a,b   Mizuno, Hiroshi ^a   Kawahara, Yoshihiro ^a   Wakimoto, Hironobu ^a,c   Ikawa, Hiroshi ^d   Kawahigashi, Hiroyuki ^a   Kanamori, Hiroyuki ^a   Matsumoto, Takashi ^a   Itoh, Takeshi ^a   Gaut, Brandon S ^b  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HITACHI LTD   (Japan)

^d MITSUBISHI SPACE SOFTWARE CO LTD   (Japan)

Author keywords

Gene duplication; Gene expression; Retroposition

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; JAPONICA; ORYZA SATIVA;

PLANT RNA;

ARABIDOPSIS; ARTICLE; GENE DUPLICATION; GENE EXPRESSION; GENETICS; HIGH THROUGHPUT SEQUENCING; PLANT GENE; RETROPOSON; RICE; SEQUENCE ANALYSIS;

ARABIDOPSIS; GENE DUPLICATION; GENE EXPRESSION; GENES, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; ORYZA SATIVA; RETROELEMENTS; RNA, PLANT; SEQUENCE ANALYSIS, RNA;

EID: 84858754773     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr111     Document Type: Article

References (68)

1. Altschul SF, et al. 1997. Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. (Pubitemid 27359211)
2. Bai Y, et al. 2007. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol. 8:R11.
3. Bai Y, et al. 2008. Evolutionary origin of regulatory regions of retrogenes in Drosophila. BMC Genomics 9:241.
4. Baucom RS, et al. 2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243-254.
5. Beilstein MA, et al. 2010. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A. 107: 18724-18728.
6. Betran E, et al. 2002. Retroposed new genes out of the X in Drosophila. Genome Res. 12:1854-1859. (Pubitemid 35469934)
7. Castillo-Davis CI, et al. 2004. cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 14:1530-1536. (Pubitemid 39193403)
8. Chaparro C, et al. 2007. RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 35:D66-D70. (Pubitemid 46056172)
9. Chenna R, et al. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500. (Pubitemid 37442184)
10. Emerson JJ, et al. 2004. Extensive gene traffic on the mammalian X chromosome. Science 303:537-540. (Pubitemid 38120854)
11. Esnault C, et al. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat Genet. 24:363-367. (Pubitemid 30187433)
12. Fawcett JA, et al. 2009. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A. 106:5737-5742.
13. Gaut BS, et al. 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A. 93:10274-10279. (Pubitemid 26314612)
14. Gu Z, et al. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:609-613. (Pubitemid 35346678)
15. Hanada K, et al. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148:993-1003. (Pubitemid 352847556)
16. Hasegawa M, et al. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174. (Pubitemid 16227864)
17. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436:793-800.
18. Jiao Y, Deng XW. 2007. A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol. 8:R28.
19. Kadota K, et al. 2003. Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. Physiol Genomics. 12:251-259. (Pubitemid 37139704)
20. Kadota K, et al. 2006. ROKU: a novel method for identification of tissue-specific genes. BMC Bioinformatics 7:294.
21. Kaessmann H, et al. 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 10:19-31.
22. Kikuchi S, et al. 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-379. (Pubitemid 36877074)
23. Koch MA, et al. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol. 17:1483-1498.
24. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
25. Li Z, et al. 2009. Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics 10(Suppl 6):S8.
26. Lincoln C, et al. 1994. A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. Plant Cell 6: 1859-1876. (Pubitemid 24986959)
27. Long M, Langley CH. 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95. (Pubitemid 23122751)
28. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
29. Ma J, Bennetzen JL. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 101:12404-12410. (Pubitemid 39122037)
30. Makova KD, Li WH. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13: 1638-1645. (Pubitemid 36874481)
31. Marques AC, et al. 2005. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3:e357.
32. Matsuda F, et al. 2010. AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol. 152:566-578.
33. Matsuoka M, et al. 1993. Expression of a rice homeobox gene causes altered morphology of transgenic plants. Plant Cell 5:1039-1048.
34. Mizuno H, et al. 2010. Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics 11:683.
35. Mondragon-Palomino M, Gaut BS. 2005. Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol Biol Evol. 22:2444-2456. (Pubitemid 41661381)
36. Mosteller F, Tukey J. 1977. Exploratory data analysis and regression. Reading (MA): Addison-Wesley.
37. Muehlbauer GJ, et al. 1999. Ectopic expression of the maize homeobox gene liguleless3 alters cell fates in the leaf. Plant Physiol. 119: 651-662. (Pubitemid 29384556)
38. Ohno S. 1970. Evolution by gene duplication. New York: Springer.
39. Okamura K, Nakai K. 2008. Retrotransposition as a source of new promoters. Mol Biol Evol. 25:1231-1238.
40. Ozawa K. 2009. Establishment of a high efficiency Agrobacterium-mediated transformation system of rice (Oryza sativa L.). Plant Sci. 176:522-527.
41. Paterson AH, et al. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A. 101:9903-9908. (Pubitemid 38869334)
42. Pearson WR, et al. 1997. Comparison of DNA sequences with protein sequences. Genomics 46:24-36. (Pubitemid 27527688)
43. Pond SL, et al. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679. (Pubitemid 40424796)
44. Potrzebowski L, et al. 2008. Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol. 6:e80.
45. Prince VE, Pickett FB. 2002. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet. 3:827-837. (Pubitemid 35303515)
46. Robinson MD, et al. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
47. Rosso L, et al. 2008a. Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein. PLoS Biol. 6:e140.
48. Rosso L, et al. 2008b. Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection. PLoS Genet. 4:e1000150.
49. Rost B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12:85-94. (Pubitemid 29103686)
50. Sachs J. 1994. Robust dual scaling with Tukey's biweight. Appl Psychol Meas. 18:301-309.
51. Schlueter JA, et al. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47:868-876. (Pubitemid 40033900)
52. Schmid M, et al. 2005. A gene expression map of Arabidopsis thaliana development. Nat Genet. 37:501-506. (Pubitemid 40617278)
53. Shiao MS, et al. 2007. Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouse. Mol Biol Evol. 24: 2242-2253.
54. Suyama M, et al. 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:W609-612. (Pubitemid 44529842)
55. Szczesniak MW, et al. 2011. Primate and rodent specific intron gains and the origin of retrogenes with splice variants. Mol Biol Evol. 28:33-37.
56. Tanaka T, et al. 2008. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36:D1028-1033.
57. Tenaillon MI, et al. 2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15:471-478.
58. Vanin EF. 1985. Processed pseudogenes: characteristics and evolution. Annu Rev Genet. 19:253-272.
59. Vinckenbosch N, et al. 2006. Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A. 103: 3220-3225. (Pubitemid 43346451)
60. Wang W, et al. 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc Natl Acad Sci U S A. 99: 4448-4453. (Pubitemid 34286005)
61. Wang W, et al. 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791-1802. (Pubitemid 44260178)
62. Wicker T, Keller B. 2007. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17:1072-1081. (Pubitemid 47026354)
63. Yamashita R, et al. 2005. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350:129-136. (Pubitemid 40719057)
64. Yu J, et al. 2005. The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 3:e38.
65. Zhang J, et al. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A. 95: 3708-3713. (Pubitemid 28173193)
66. Zhang Y, et al. 2005. Computational identification of 69 retroposons in Arabidopsis. Plant Physiol. 138:935-948. (Pubitemid 43793170)
67. Zhang Z, et al. 2002. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res. 12: 1466-1482. (Pubitemid 35189531)
68. Zhu Z, et al. 2009. Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol. 151:1943-1951.