Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Lopes, Fabrício R ^a   Jjingo, Daudi ^b   Da Silva, Carlos R M ^c   Andrade, Alan C ^d   Marraccini, Pierre ^d,e   Teixeira, João B ^d   Carazzolle, Marcelo F ^f   Pereira, Gonçalo A G ^f   Pereira, Luiz Filipe P ^d   Vanzela, André L L ^c   Wang, Lu ^b   King Jordan, I ^b,g   Carareto, Claudia M A ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c STATE UNIVERSITY OF LONDRINA   (Brazil)

^d EMBRAPA CERRADOS   (Brazil)

^e UMR AGAP   (France)

^f UNIVERSITY OF CAMPINAS   (Brazil)

^g PanAmerican Bioinformatics Institute   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; COFFEE; COFFEE CANEPHORA; COFFEE EUGENOIDES; CULTIVAR; DROUGHT STRESS; DROUGHT TOLERANCE; EXON; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PLANT GROWTH; TRANSPOSON;

CHROMOSOMES, PLANT; COFFEA; DNA TRANSPOSABLE ELEMENTS; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; TRANSCRIPTION, GENETIC;

EID: 84893022040     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078931     Document Type: Article

References (49)

1. Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 19: 68-72.
2. Thornburg BG, Gotea V, Makalowski W (2006) Transposable elements as a significant source of transcription regulating signals. Gene 365: 104-110.
3. Zhang J, Peterson T (1999) Genome rearrangements by nonlinear transposons in maize. Genetics 153: 1403-1410.
4. Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci U S A 94: 7704-7711.
5. Fedoroff N (2000) Transposons and genome evolution in plants. Proc Natl Acad Sci U S A 97: 7002-7007.
6. Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36.
7. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
8. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
9. Zaratiegui M, Irvine DV, Martienssen RA (2007) Noncoding RNAs and gene silencing. Cell 128: 763-776.
10. Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, et al. (2007) Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 49: 38-45.
11. Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33: 102-106.
12. Biemont C (2009) Are transposable elements simply silenced or are they under house arrest? Trends Genet 25: 333-334.
13. Okamoto H, Hirochika H (2001) Silencing of transposable elements in plants. Trends Plant Sci 6: 527-534.
14. Grandbastien MA (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3: 181-187.
15. Pouteau S, Huttner E, Grandbastien MA, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10: 1911-1918.
16. Hirochika H (1993) Activation of tobacco retrotransposons during tissue-culture. EMBO J 12: 2521-2528.
17. de Araujo PG, Rossi M, de Jesus EM, Saccaro NL Jr, Kajihara D, et al. (2005) Transcriptionally active transposable elements in recent hybrid sugarcane. Plant J 44: 707-717.
18. Vicient CM (2010) Transcriptional activity of transposable elements in maize. BMC Genomics 11: 601.
19. Lashermes P, Andrade AC, Etienne H (2008) Genomics of coffee, one of the world's largest traded commodities. In: Moore H, Ming R, editors. Genomics of Tropical Crop Plants: Springer. 203-226.
20. Lashermes P, Combes MC, Robert J, Trouslot P, D'Hont A, et al. (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 61: 259-266.
21. Leroy T, Ribeyre F, Bertrand B, Charmetant P, Dufour M, et al. (2006) Genetics of coffee quality. Brazilian Plant Physiology 18: 229-242.
22. Lopes FR, Carazzolle MF, Pereira GA, Colombo CA, Carareto CM (2008) Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants. Mol Genet Genomics 279: 385-401.
23. Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, et al. (2009) Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes. BMC Plant Biol 25: 9-22.
24. Dubreuil-Tranchant C, Guyot R, Guellim A, Duret C, de la Mare M, et al. (2011) Site-specific insertion polymorphism of the MITE Alex-1 in the Genus Coffea suggests interspecific gene flow. Int J Evol Biol 2011: 358412.
25. Hamon P, Duroy PO, Dubreuil-Tranchant C, Mafra D'Almeida Costa P, Duret C, et al. (2011) Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genomics 285: 447-460.
26. Cenci A, Combes MC, Lashermes P (2012) Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments. Plant Mol Biol 78: 135-145.
27. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
28. Brogna S, Wen J (2009) Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol 16: 107-113.
29. Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 36: 1073-1078.
30. Yuyama PM, Pereira LF, Santos TB, Sera T, Vilas-Boas LA, et al. (2012) FISH using a gag -like fragment probe reveals a common Ty3-gypsy -like retrotransposon in genome of Coffea species. Genome 55: 825-833.
31. Courtial B, Feuerbach F, Eberhard S, Rohmer L, Chiapello H, et al. (2001) Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana, and transposed copies integrate into genes. Mol Genet Genomics 265: 32-42.
32. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A 93: 7783-7788.
33. Feldman M, Levy AA (2005) Allopolyploidy - a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109: 250-258.
34. Feldman M, Levy AA (2012) Genome evolution due to allopolyploidization in wheat. Genetics 192: 763-774.
35. Voytas DF, Naylor GJ (1998) Rapid flux in plant genomes. Nature Genetics 20: 6-7.
36. Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, et al. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J 41: 221-230.
37. Meyers BC, Tingley SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11: 1660-1676.
38. Rossi M, de Araujo PG, Van Sluys MA (2001) Survey of transposable elements in sugarcane expressed sequence tags (ESTs). Genet Mol Biol 24: 147-154.
39. Bacci Jr M, Soares RBS, Tajara E, Ambar G, Fischer CN, et al. (2005) Identification and frequency of transposable elements in Eucalyptus. Genet Mol Biol 28: 634-639.
40. Beguiristain T, Grandbastien MA, Puigdomènech P, Casacuberta JM (2001) Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol 127: 212-221.
41. Ferrão RG, Fonseca AFA, Ferrão MAV, Silveira JSM, Bragança SM, et al. (2000) EMCAPA 8141 - Robustão Capixaba, variedade clonal de caféconilon tolerante à seca, desenvolvida para o estado do Espírito Santo. Revista Ceres 273: 555-560.
42. Marraccini P, Vinecky F, Alves GS, Ramos HJ, Elbelt S, et al. (2012) Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora . J Exp Bot 63: 4191-4212.
43. Mondego JM, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GG, Pereira LF, Andrade AC, Colombo CA, Vieira LG, Pereira GA; Brazilian Coffee Genome Project Consortium (2011). An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora . BMC Plant Biol 11: 30.
44. Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Pétiard V, et al. (2005) Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 112: 114-130.
45. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
46. Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK (2007) Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct 2: 31.
47. Freire LP, Marraccini P, Rodrigues GC, Andrade AC (2013) Análise da expressão do gene da manose-6-fosfato redutase em folhas de plantas de café (Coffea arabica) submetidas ao estresse hídrico no campo. Coffee Sci 8: 17-23.
48. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
49. Heslop-Harrison JS, Schwarzacher T (1991) In situ hybridization with automated chromosome denaturation. Technique 3: 109-116.