LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

DNA Research

Volumn 22, Issue 1, 2015, Pages 91-100

  Barghini, Elena ^a   Natali, Lucia ^a   Giordani, Tommaso ^a   Cossu, Rosa Maria ^a,b   Scalabrin, Simone ^c   Cattonaro, Federica ^c   Šimková, Hana ^d   Vrána, Jan ^d   Doležel, Jaroslav ^d   Morgante, Michele ^e,f   Cavallini, Andrea ^a  

^a UNIVERSITY OF PISA   (Italy)

^b SCUOLA SUPERIORE SANT ANNA   (Italy)

^c Applied Genomics Institute   (Italy)

^d PALACKÝ UNIVERSITY   (Czech Republic)

^e UNIVERSITY OF UDINE   (Italy)

^f Applied Genomics Institute   (Italy)

Author keywords

BAC sequencing; Insertion age; LTR retrotransposons; Next generation sequencing; Olive

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; DNA SEQUENCE; GENETIC DISTANCE; LONG TERMINAL REPEAT; MOLECULAR CLOCK; MUTATION RATE; NONHUMAN; OLIVE TREE; PHYLOGENETIC TREE; PHYLOGENY; PLANT GENOME; PROTEIN DOMAIN; RETROPOSON; TANDEM REPEAT; TRANSPOSON; CHROMOSOME MAP; GENETIC ASSOCIATION; GENETICS;

RETROPOSON;

CHROMOSOME MAPPING; GENOME-WIDE ASSOCIATION STUDY; OLEA; RETROELEMENTS; TERMINAL REPEAT SEQUENCES;

EID: 84941567657     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsu042     Document Type: Article

References (55)

1. Stark, A.H. and Madar, Z. 2002, Olive oil as a functional food: epidemiology and nutritional approaches, Nutrition Rev., 60, 170-6.
2. Sarri, V., Baldoni, L., Porceddu, A., et al. 2006, Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations, Genome, 49, 1606-15.
3. Besnard, G., Baradat, P. and Bervillé, A. 2001, Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars, Theor. Appl. Genet., 102, 251-8.
4. Loureiro, J., Rodriguez, E., Costa, A. and Santos, C. 2007, Nuclear DNA content estimations in wild olive (Olea europaea L. ssp. europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry, Genet. Res. Crop Evol., 54, 21-5.
5. Katsiotis, A., Hagidimitriou, M., Douka, A. and Hatzopoulos, P. 1998, Genomic organization, sequence interrelationship, and physical localization using in situ hybridization of two tandemly repeated DNA sequences in the genus Olea, Genome, 41, 527-34.
6. Bitonti, M.B., Cozza, R., Chiappetta, A., et al. 1999, Amount and organization of the heterochromatin in Olea europaea and related species, Heredity, 83, 188-95.
7. Lorite, P., Garcia, M.F., Carrillo, J.A. and Palomeque, T. 2001, A new repetitive DNA sequence family in the olive (Olea europaea L), Hereditas, 134, 73-8.
8. Stergiou, G., Katsiotis, A., Hagidimitriou, M. and Loukas, M. 2002, Genomic and chromosomal organization of Ty1-Copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements, Theor. Appl. Genet., 104, 926-33.
9. Natali, L., Giordani, T., Buti, M. and Cavallini, A. 2007, Isolation of Ty1-Copia putative LTR sequences and their use as a tool to analyse genetic diversity in Olea europaea, Mol. Breed., 19, 255-65.
10. Jiao, Y., Leebens-Mack, J., Ayyampalayam, S., et al. 2012, A genome triplication associated with early diversification of the core eudicots, Genome Biol., 13, R3.
11. Hawkins, J.S., Kim, H.R., Nason, J.D., Wing, R.A. and Wendel, J.F. 2006, Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium, Genome Res., 16, 1252-61.
12. Kumar, A. and Bennetzen, J.B. 1999, Plant retrotransposons, Ann. Rev. Genet., 33, 479-532.
13. Beguiristain, T., Grandbastien, M.A., Puigdomenech, P. and Casacuberta, J. M. 2001, Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants, Plant Physiol., 127, 212-21.
14. Brunner, S., Fengler, K., Morgante, M., Tingey, S. and Rafalski, A. 2005, Evolution of DNA sequence nonhomologies among maize inbreds, Plant Cell, 17, 343-60.
15. Paterson, A.H., Bowers, J.E., Bruggmann, R., et al. 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551-6.
16. Buti, M., Giordani, T., Cattonaro, F., et al. 2011, Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions, Theor. Appl. Genet., 123, 779-91.
17. Cossu, R.M., Buti, M., Giordani, T., Natali, L. and Cavallini, A. 2012, A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome, Tree Genet. Genomes, 8, 61-75.
18. Barghini, E., Natali, L., Cossu, R.M., et al. 2014, The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome, Genome Biol. Evol., 6, 776-91.
19. SanMiguel, P., Gaut, B.S., Tikhonov, A., et al. 1998, The paleontology of intergene retrotransposons of maize, Nat. Genet., 20, 43-5.
20. Doležel, J., Číhalíková, J. and Lucretti, S. 1992, A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L., Planta, 188, 93-8.
21. Šimková, H., Číhalíková, J., Vrána, J., Lysák, M.A. and Doležel, J. 2003, Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips, Biol. Plant, 46, 369-73.
22. Šimková, H., Šafář, J., Kubaláková, M., et al. 2011, BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes, J. Biomed. Biotechnol., 20, 11, 302543.
23. Martin, M. 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J., 17, 10-12.
24. Simpson, J.T., Wong, K., Jackman, S.D., et al. 2009, ABySS: a parallel assembler for short read sequence data, Genome Res., 19, 1117-23.
25. Xu, Z. and Wang, H. 2007, LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucl. Acids Res., 35, W265-8.
26. Sonnhammer, E.L. and Durbin, R. 1995, A dot-matriprogram with dynamic threshold control suited for genomic DNA and protein sequence analysis, Gene, 167, GC1-GC10.
27. Thompson, J.D., Higgins, D.G. and Gibson, T.J. 1994, CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucl. Acids Res., 22, 4673-80.
28. Munoz-Merida, A., González-Plaza, J.J., Cañada, A., et al. 2013, De novo assembly and functional annotation of the olive (Olea europaea) transcriptome, DNA Res., 20, 93-108.
29. Nei, M. and Gojobori, T. 1986, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions, Mol. Biol. Evol., 3, 418-26.
30. Rozas, J. and Rozas, R. 1999, DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis, Bioinformatics, 15, 174-5.
31. Besnard, G., Rubio de Casas, R., Christin, P.A. and Vargas, P. 2009, Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: tertiary climatic shifts and lineage differentiation times, Ann. Bot., 104, 143-60.
32. Ma, J. and Bennetzen, J.L. 2004, Rapid recent growth and divergence of rice nuclear genomes, Proc. Natl. Acad. Sci. USA, 101, 12404-10.
33. Jurka, J., Kapitonov, V.V., Pavlicek, A., et al. 2005, Repbase Update, a database of eukaryotic repetitive elements, Cytogenet. Genome Res., 110, 462-7.
34. Gorinsek, B., Gubensek, F. and Kordis, D. 2004, Evolutionary genomics of chromoviruses in eukaryotes, Mol. Biol. Evol., 21, 781-98.
35. Nystedt, B., Nathaniel, R., Street, N.R., et al. 2013, The Norway spruce genome sequence and conifer genome evolution, Nature, 497, 579-84.
36. Gaut, B.S. 1998, Molecular clocks and nucleotide substitution rates in higher plants. In:Hecht, M.K., Macintyre, R.J. and Clegg, M.T. (eds.), Evolutionary Biology, vol. 30. Plenum Press, New York, pp. 93-120.
37. Huang, S., Li, R., Zhang, Z., et al. 2009, The genome of the cucumber, Cucumis sativus L., Nat. Genet., 41, 1275-81.
38. Schnable, P.S., Ware, D., Fulton, R.S., et al. 2009, The B73 maize genome: complexity, diversity, and dynamics, Science, 326, 1112-5.
39. Vitte, C., Fustier, M.A., Alix, K. and Tenaillon, M.I. 2014, The bright side of transposons in crop evolution, Brief. Funct. Genomics, doi:10.1093/bfgp/elu002.
40. Ming, R., Hou, S., Feng, Y., et al. 2008, The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus), Nature, 452, 991-7.
41. The French-Italian Public Consortium for Grape Genome Characterization 2007, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, 449, 463-7.
42. Neumann, P., Navrátilová, A., Koblížková, A., et al. 2011, Plant centromeric retrotransposons: a structural and cytogenetic perspective, Mobile DNA, 2, 4.
43. Ma, J., Devos, K.M. and Bennetzen, J.L. 2004, Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice, Genome Res., 14, 860-9.
44. Ammiraju, J.S., Zuccolo, A., Yu, Y., et al. 2007, Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza, Plant J., 52, 342-51.
45. Morse, A.M., Peterson, D.G., Islam-Faridi, M.N., et al. 2009, Evolution of genome size and complexity in Pinus, PLoS ONE, 4, e4332.
46. Cavallini, A., Natali, L., Zuccolo, A., et al. 2010, Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome, Theor. Appl. Genet., 120, 491-508.
47. Natali, L., Cossu, R.M., Barghini, E., et al. 2013, The repetitive component of the sunflower genome as revealed by different procedures for assembling next generation sequencing reads, BMC Genomics, 14, 686.
48. Zuccolo, A., Sebastian, A., Yu, Y., et al. 2010, Assessing the extent of substitution rate variation of retrotransposon long terminal repeat sequences in Oryza sativa and Oryza glaberrima, Rice, 3, 242-50.
49. Ungerer, M.C., Strakosh, S.C. and Stimpson, K.M. 2009, Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data, BMC Biol., 7, 40.
50. Vukich, M., Schulman, A.H., Giordani, T., et al. 2009, Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers, Theor. Appl. Genet., 119, 1027-38.
51. Baucom, R.S., Estill, J.C., Leebens-Mack, J. and Bennetzen, J.L. 2009, Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome, Genome Res., 19, 243-54.
52. Lisch, D. 2009, Epigenetic regulation of transposable elements in plants, Ann. Rev. Plant Biol., 60, 43-66.
53. Baucom, R.S., Estill, J.C., Chaparro, C., et al. 2009, Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome, PLoS Genet., 5, e1000732.
54. Le Rouzic, A., Dupas, S. and Capy, P. 2007, Genome ecosystem and transposable elements species, Gene, 390, 214-20.
55. Venner, S., Feschotte, C. and Biemont, C. 2009, Dynamics of transposable elements: towards a community ecology of the genome, Trends Genet., 25, 317-23.