Arguments for standardizing transposable element annotation in plant genomes

Trends in Plant Science

Volumn 18, Issue 7, 2013, Pages 367-376

  Ragupathy, Raja ^a,b   You, Frank M ^a   Cloutier, Sylvie ^a,b  

^a Cereal Research Centre   (Canada)

^b UNIVERSITY OF MANITOBA   (Canada)

Author keywords

Annotation; Epigenetics; Non Mendelian inheritance; Plant genome; Retroelement; Transposable element

Indexed keywords

BREEDING; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MOLECULAR GENETICS; PLANT GENOME; REVIEW; TRANSPOSON;

BREEDING; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE ANNOTATION;

EID: 84880787525     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2013.03.005     Document Type: Review

References (110)

1. McClintock B. The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. U.S.A. 1950, 36:344-355.
2. Lisch D. How important are transposons for plant evolution?. Nat. Rev. Genet. 2013, 14:49-61.
3. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. Arabidopsis Genome Sequencing Consortium.
4. Metzker M.L. Sequencing technologies: the next generation. Nat. Rev. Genet. 2010, 11:31-46.
5. Treangen T.J., Salzberg S.L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 2012, 13:36-46.
6. Alkan C., et al. Limitations of next generation genome sequence assembly. Nat. Methods 2011, 8:61-65.
7. Bennetzen J. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr. Opin. Genet. Dev. 2005, 15:621-627.
8. Vitte C., Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase or decrease model. Cytogenet. Genome Res. 2005, 110:91-107.
9. Cordaux R., Batzer M.A. The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 2009, 10:691-703.
10. Schnable P.S., et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115.
11. Choulet F., et al. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 2010, 22:1686-1701.
12. Bucher E., et al. Epigenetic control of transposon transcription and mobility in Arabidopsis. Curr. Opin. Plant Biol. 2012, 15:1-8.
13. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
14. Morales-Ruiz T., et al. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:6853-6858.
15. Saze H., et al. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 2003, 34:65-69.
16. Slotkin R.K., et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136:461-472.
17. Calarco J.P., et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012, 151:194-205.
18. Ibarra C.A., et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 2012, 337:1360-1364.
19. McClintock B. The significance of responses of the genome to challenge. Science 1984, 226:792-801.
20. Grandbastien M-A. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 1998, 3:181-187.
21. Wessler S.R. Plant retrotransposons: turned on by stress. Curr. Biol. 1996, 6:959-961.
22. Kalendar R., et al. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimate divergence. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:6603-6607.
23. Ito H., et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 2011, 472:115-119.
24. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. The ENCODE Project Consortium.
25. Zhang X., et al. Role of RNA polymerase IV in plant small RNA metabolism. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:4536-4541.
26. Kim E-D., Sung S. Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci. 2011, 17:16-21.
27. Gutzat R., Scheid O.M. Epigenetic responses to stress: triple defense. Curr. Opin. Plant Biol. 2012, 15:1-6.
28. Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 2007, 8:272-285.
29. Kashkush K., Khasdan V. Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 2007, 177:1975-1985.
30. Tapia G., et al. Involvement of ethylene in stress-induced expression of the TLC1.1 retrotransposon from Lycopersicon chilense Dun. Plant Physiol. 2005, 138:2075-2086.
31. Takeda S., et al. A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant J. 1999, 18:383-393.
32. Lisch D., Bennetzen J.L. Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 2011, 14:156-161.
33. McCue A.D., Slotkin R.K. Transposable element small RNAs as regulators of gene expression. Trends Genet. 2012, 28:616-623.
34. Piriyapongsa J., Jordan I.K. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 2008, 14:814-821.
35. Li Y., et al. Domestication of transposable elements into microRNA genes in plants. PLoS ONE 2011, 6:e19212.
36. Calarco J.P., Martienssen R.A. Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr. Opin. Genet. Dev. 2011, 21:134-139.
37. Borchert G.M., et al. Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive element origins. Mob. Genet. Elements 2011, 1:8-17.
38. Feschotte C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 2008, 9:397-405.
39. Lee T., et al. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 2012, 7:781-795.
40. Soppe W.J.J., et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 2000, 6:791-802.
41. Brachi B., et al. Genome wide association studies in plants: the missing heritability is in the field. Genome Biol. 2011, 12:232.
42. Deal R.B., Henikoff S. Histone variants and modifications in plant gene regulation. Curr. Opin. Plant Biol. 2011, 14:116-122.
43. Paszkowski J., Grossniklaus U. Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Curr. Opin. Plant Biol. 2011, 14:1-9.
44. Mirouze M., Paszkowski J. Epigenetic contribution to stress adaptation in plants. Curr. Opin. Plant Biol. 2011, 14:267-274.
45. Richards E.J. Natural epigenetic variation in plant species: a view from the field. Curr. Opin. Plant Biol. 2011, 14:204-209.
46. Schmitz R.J., et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011, 334:369-373.
47. Jurka J., et al. Repetitive sequences in complex genomes: structure and evolution. Annu. Rev. Genomics Hum. Genet. 2007, 8:241-259.
48. Wicker T., et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 2007, 8:973-982.
49. Makalowski W., et al. Transposable elements and their identification. Evolutionary Genomics: Statistical and Computational Methods 2012, 337-359. Humana Press. M. Anisimova (Ed.).
50. Bao Z., Eddy S.R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002, 12:1269-1276.
51. Li R., et al. ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput. Biol. 2005, 1:e43.
52. Kurtz S., et al. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 2008, 9:517.
53. Novák P., et al. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 2010, 11:378.
54. Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity 2010, 104:520-533.
55. Goecks J., et al. Galaxy: a comprehensive approach for supporting accessible, reproducible and transparent computational research in the life sciences. Genome Biol. 2010, 11:R86.
56. Goff S.A., et al. The iPlant Collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2011, 2. Article 34.
57. Bergman C.M., Quesneville H. Discovering and detecting transposable elements in genome sequences. Brief. Bioinform. 2007, 8:382-392.
58. Flutre T., et al. Considering transposable element diversification in de novo annotation approaches. PLoS ONE 2011, 6:e16526.
59. Flutre T., et al. In search of lost trajectories: recovering the diversification of transposable elements. Mob. Genet. Elements 2011, 1:151-154.
60. Permal E., et al. Roadmap for annotating transposable elements in eukaryote genomes. Mobile Genetic Elements: Protocols and Genomic Applications 2012, 53-67. Humana Press. W.J. Miller, P. Capy (Eds.).
61. Lowe C., Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS ONE 2012, 7:e43128.
62. Naito K., et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009, 461:1130-1134.
63. Gao D., et al. A highly conserved small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS ONE 2012, 7:e32010.
64. Miyao A., et al. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon rich regions of the genome. Plant Cell 2003, 15:1771-1780.
65. Studer A., et al. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 2011, 43:1160-1163.
66. Tuskan G.A., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604.
67. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449:463-467. French-Italian Public Consortium for Grapevine Genome Characterization.
68. Ming R., et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya L.). Nature 2008, 452:991-996.
69. Huang S., et al. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 2009, 41:1275-1281.
70. Chan A.P., et al. Draft genome sequence of the oilseed species Ricinus communis. Nat. Biotechnol. 2010, 28:951-956.
71. Schmutz J., et al. Genome sequence of the palaeopolyploid soybean. Nature 2010, 463:178-183.
72. Young N.D., et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480:520-524.
73. Velasco R., et al. The genome of the domesticated apple (Malus domestica Borkh.). Nat. Genet. 2010, 42:833-839.
74. Hu T.T., et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 2011, 43:476-481.
75. Wang X., et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43:1035-1039.
76. Shulaev V., et al. The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 2011, 43:109-116.
77. Argout X., et al. The genome of Theobroma cacao. Nat. Genet. 2011, 43:101-108.
78. Genome sequence and analysis of the tuber crop potato. Nature 2011, 475:189-195. The Potato Genome Sequencing Consortium.
79. Varshney R.K., et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 2012, 30:83-89.
80. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485:635-641. The Tomato Genome Consortium.
81. Wang Z., et al. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J. 2012, 72:461-473.
82. Wang K., et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 2012, 44:1098-1103.
83. Paterson A.H., et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 2012, 492:423-427.
84. Xu Q., et al. The draft genome of sweet orange (Citrus sinensis). Nat. Genet. 2013, 45:59-66.
85. Garcia-Mas J., et al. The genome of melon (Cucumis melo L.). Proc. Nat. Acad. Sci. U.S.A. 2012, 109:11872-11877.
86. Wu J., et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013, 23:396-408.
87. Varshney R.K., et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 2013, 31:240-246.
88. The map-based sequence of the rice genome. Nature 2005, 436:793-800. International Rice Genome Sequencing Consortium.
89. Paterson A.H., et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457:551-556.
90. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768. The International Brachypodium Initiative.
91. Al-Dous E.K., et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat. Biotechnol. 2011, 29:521-527.
92. Bennetzen J.L., et al. Reference genome sequence of the model plant Setaria. Nat. Biotechnol. 2012, 30:555-561.
93. Zhang G., et al. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat. Biotechnol. 2012, 30:549-554.
94. D'Hont A., et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012, 488:213-217.
95. A physical, genetic and functional sequence assembly of the barley genome. Nature 2012, 491:711-716. The International Barley Genome Sequencing Consortium.
96. Pecinka A., et al. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 2010, 22:3118-3129.
97. Mirouze M., et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 2009, 461:427-430.
98. Tsukahara S., et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 2009, 461:423-426.
99. Miura A., et al. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 2001, 411:212-214.
100. Ramallo E., et al. Reme1, a copia retrotransposon in melon, is transcriptionally induced by UV light. Plant Mol. Biol. 2008, 66:137-150.
101. Petit M., et al. Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol. 2010, 186:135-147.
102. Melayah D., et al. The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant J. 2001, 28:159-168.
103. Grandbastien M-A., et al. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 1989, 337:376-380.
104. Rajput M.K., Upadhyaya K.C. Isolation and characterization of stress induced Ty-1-copia like retrotransposable elements in chickpea (Cicer arietinum L.). Mol. Biol. 2010, 44:693-698.
105. Woodrow P., et al. Polymorphism of a new Ty-1 copia retrotransposon in durum wheat under salt and light stresses. Theor. Appl. Genet. 2010, 121:311-322.
106. Woodrow P., et al. Ttd1a promoter is involved in DNA-protein binding by salt and light stress. Mol. Biol. Rep. 2011, 38:3787-3794.
107. Picault N., et al. Identification of an active LTR retrotransposon in rice. Plant J. 2009, 58:754-765.
108. Nakazaki T., et al. Mobilization of a transposon in the rice genome. Nature 2003, 421:170-172.
109. Kikuchi K., et al. The plant MITE mPing is mobilized in anther culture. Nature 2003, 421:167-169.
110. Kimura Y., et al. OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol. 2001, 42:1345-1354.