A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

Tree Genetics and Genomes

Volumn 11, Issue 5, 2015, Pages

  Natali, Lucia ^a   Cossu, Rosa Maria ^a,b   Mascagni, Flavia ^a   Giordani, Tommaso ^a   Cavallini, Andrea ^a  

^a UNIVERSITY OF PISA   (Italy)

^b SCUOLA SUPERIORE SANT ANNA   (Italy)

Author keywords

Copia; Gypsy; LTR retrotransposon lineages; Poplar genome; Populus trichocarpa

Indexed keywords

EID: 84942433862     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-015-0937-z     Document Type: Article

References (51)

1. Barghini E, Natali L, Cossu RM, Giordani T, Pindo M, Cattonaro F, Scalabrin S, Velasco R, Morgante M, Cavallini A (2014) The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. Genome Biol Evol 6:776–791
2. Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A (2015) LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Res 22:91–100
3. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, SanMiguel PJ, Bennetzen JL (2009a) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732. doi:10.1371/journal.pgen.1000732
4. Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL (2009b) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res 19:243–254
5. Bennetzen JL, Kellogg EA (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9:1509–1514
6. Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343–360
7. Buti M, Giordani T, Cattonaro F, Cossu RM, Pistelli L, Vukich M, Morgante M, Cavallini A, Natali L (2011) Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. Theor Appl Genet 123:779–791
8. Cavallini A, Natali L, Zuccolo A, Giordani T, Jurman I, Ferrillo V, Vitacolonna N, Sarri V, Cattonaro F, Ceccarelli M, Cionini PG, Morgante M (2010) Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. Theor Appl Genet 120:491–508
9. Charles M, Belcram H, Just J, Huneau C, Viollet A, Couloux A, Segurens B, Carter M, Huteau V, Coriton O, Appels R, Samain S, Chalhoub B (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 180:1071–1086
10. Cossu RM, Buti M, Giordani T, Natali L, Cavallini A (2012) A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome. Tree Genet Genomes 8:61–75
11. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079
12. Gorinsek B, Gubensek F, Kordis D (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol Biol Evol 21:781–798
13. Hawkins JS, Kim HR, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16:1252–1261
14. Islam-Faridi MN, Nelson CD, DiFazio SP, Gunter LE, Tuskan GA (2009) Cytogenetic analysis of Populus trichocarpa—ribosomal DNA, telomere repeat sequence, and marker-selected BACs. Cytogenet Genome Res 125:74–80
15. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467
16. Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoyb A, Schulman AH (2004) Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166:1437–1450
17. Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33:102–106
18. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
19. Le Rouzic A, Dupas S, Capy P (2007) Genome ecosystem and transposable elements species. Gene 390:214–220
20. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079
22. Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A (2011) The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39:D70–D74
23. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101:12404–12410
24. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14:860–869
25. Moisy C, Garrison KE, Meredith CP, Pelsy F (2008) Characterization of ten novel Ty1/Copia-like retrotransposon families of the grapevine genome. BMC Genomics 9:469
26. Natali L, Cossu RM, Barghini E, Giordani T, Buti M, Mascagni F, Morgante M, Gill N, Kane NC, Rieseberg L, Cavallini A (2013) The repetitive component of the sunflower genome as revealed by different procedures for assembling next generation sequencing reads. BMC Genomics 14:686
27. Neumann P, Požárková D, Macas J (2003) Highly abundant pea LTR-retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol Biol 53:399–410
28. Neumann P, Navrátilová A, Koblížková A, Kejnovský E, Hřibová E, Hobza R, Widmer A, Doležel J, Macas J (2011) Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA 2:4
29. Novak P, Neumann P, Pech J, Steinhaisl J, Macas J (2013) RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence reads. Bioinformatics 29:792–793
30. Nystedt B, Nathaniel R, Street NR et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584
31. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A Ty3/gypsy retrotransposon-like sequence localized to the centromeric regions of cereal chromosomes. Plant J 16:721–728
32. Rajagopal J, Das S, Khurana DK, Srivastava PS, Lakshmikumaran M (1999) Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus. Genome 42:909–918
33. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16:276–277
34. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45
35. Santini S, Cavallini A, Natali L, Minelli S, Maggini F, Cionini PG (2002) Ty1/Copia- and Ty3/Gypsy-like DNA sequences in Helianthus species. Chromosoma 111:192–200
36. Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF et al (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196:713–725
37. Sonnhammer EL, Durbin R (1995) A dot-matriprogram with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1–GC10
38. Tian Z, Rizzon C, Du JC, Zhu L, Bennetzen JL, Jackson SA, Gaut BS, Ma J (2009) Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res 19:2221–2230
39. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604
40. Ungerer MC, Strakosh SC, Stimpson KM (2009) Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data. BMC Biol 7:40
41. Venner S, Feschotte C, Biemont C (2009) Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 25:317–323
42. Vitte C, Fustier MA, Alix K, Tenaillon MI (2014) The bright side of transposons in crop evolution. Brief Funct Genomics. doi:10.1093/bfgp/elu002
43. Vukich M, Schulman AH, Giordani T, Natali L, Kalendar R, Cavallini A (2009) Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers. Theor Appl Genet 119:1027–1038
44. Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci U S A 103:17644–17649
45. Weber B, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T (2013) Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration. Mob DNA 4:8
46. 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
47. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982
48. Wright DA, Voytas DF (2002) Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res 12:122–131
49. Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35:W265–W268
50. Zhou F, Xu Y (2009) RepPop: a database for repetitive elements in Populus trichocarpa. BMC Genomics 10:14
51. Zuccolo A, Sebastian A, Yu Y, Jackson S, Rounsley S, Billheimer D, Wing RA (2010) Assessing the extent of substitution rate variation of retrotransposon long terminal repeat sequences in Oryza sativa and Oryza glaberrima. Rice 3:242–250