Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Jiang, Feng ^a   Yang, Meiling ^a,b   Guo, Wei ^a   Wang, Xianhui ^a   Kang, Le ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b SHANXI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; IMAGO; LOCUST; LONG TERMINAL REPEAT; MIGRATORY SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROCESS DEVELOPMENT; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSPORT; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TRANSCRIPTOMICS; TRANSPOSON;

ANIMALS; CONSENSUS SEQUENCE; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ORDER; LOCUSTA MIGRATORIA; PHYLOGENY; RETROELEMENTS; RNA-DIRECTED DNA POLYMERASE; TERMINAL REPEAT SEQUENCES; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EUKARYOTA; HEXAPODA; LOCUSTA MIGRATORIA;

EID: 84863669014     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040532     Document Type: Article

References (77)

1. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, et al. (2007) Eukaryotic genome size databases. Nucleic Acids Res 35: D332-338.
2. Dufresne F, Jeffery N, (2011) A guided tour of large genome size in animals: what we know and where we are heading. Chromosome research pp. 1-14.
3. 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.
4. Capy P, (2005) Classification and nomenclature of retrotransposable elements. Cytogenet Genome Res 110: 457-461.
5. Cordaux R, Batzer MA, (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
6. Arkhipova I, Meselson M, (2005) Deleterious transposable elements and the extinction of asexuals. BioEssays 27: 76-85.
7. Hawkins JS, Proulx SR, Rapp RA, Wendel JF, (2009) Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci U S A 106: 17811-17816.
8. Feschotte C, (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405.
9. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
10. Dooner HK, He L, (2008) Maize genome structure variation: interplay between retrotransposon polymorphisms and genic recombination. Plant Cell 20: 249-258.
11. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, et al. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316: 1718-1723.
12. Novick PA, Basta H, Floumanhaft M, McClure MA, Boissinot S, (2009) The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals. Mol Biol Evol 26: 1811-1822.
13. Gregory TR, (2005) The C-value enigma in plants and animals: a review of parallels and an appeal for partnership. Annals of Botany 95: 133-146.
14. Guo B, Zou M, Gan X, He S, (2010) Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing. BMC Genomics 11: 396.
15. Guo W, Wang XH, Zhao DJ, Yang PC, Kang L, (2010) Molecular cloning and temporal-spatial expression of I element in gregarious and solitary locusts. J Insect Physiol 56: 943-948.
16. Kojima KK, Kapitonov VV, Jurka J, (2011) Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol 28: 17-20.
17. Biedler J, Tu Z, (2003) Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity. Mol Biol Evol 20: 1811-1825.
18. Wang S, Lorenzen MD, Beeman RW, Brown SJ, (2008) Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biol 9: R61.
19. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
20. Xu AG, He L, Li Z, Xu Y, Li M, et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol 6: e1000843.
21. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
22. Levin HL, Moran JV, (2011) Dynamic interactions between transposable elements and their hosts. Nature Reviews Genetics 12: 615-627.
23. Beraldi R, Pittoggi C, Sciamanna I, Mattei E, Spadafora C, (2006) Expression of LINE-1 retroposons is essential for murine preimplantation development. Molecular reproduction and development 73: 279-287.
24. Faunes F, Sanchez N, Moreno M, Olivares GH, Lee-Liu D, et al. (2011) Expression of transposable elements in neural tissues during Xenopus development. PLoS One 6: e22569.
25. Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, et al. (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell 7: 597-606.
26. Minervini CF, Viggiano L, Caizzi R, Marsano RM, (2009) Identification of novel LTR retrotransposons in the genome of Aedes aegypti. Gene 440: 42-49.
27. Parkhurst S, Corces VG, (1987) Developmental expression of Drosophila melanogaster retrovirus-like transposable elements. The EMBO Journal 6: 419.
28. Brookman JJ, Toosy AT, Shashidhara L, White R, (1992) The 412 retrotransposon and the development of gonadal mesoderm in Drosophila. Development 116: 1185-1192.
29. Moczek AP, (2010) Phenotypic plasticity and diversity in insects. Philos Trans R Soc Lond B Biol Sci 365: 593-603.
30. Slotkin RK, Martienssen R, (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
31. Kazazian HH Jr, (2004) Mobile elements: drivers of genome evolution. Science 303: 1626-1632.
32. Whitelaw E, Martin DIK, (2001) Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nat Genet 27: 361-365.
33. Tomilin NV, (2008) Regulation of mammalian gene expression by retroelements and non-coding tandem repeats. BioEssays 30: 338-348.
34. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E, (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.
35. Clegg MT, Durbin ML, (2000) Flower color variation: a model for the experimental study of evolution. Proc Natl Acad Sci U S A 97: 7016-7023.
36. Mansour A, (2007) Epigenetic activation of genomic retrotransposons. Journal of Cell and Molecular Biology 6: 99-107.
37. Guo W, Wang X, Ma Z, Xue L, Han J, et al. (2011) CSP and Takeout genes modulate the switch between attraction and repulsion during behavioral phase change in the migratory locust. PLoS genetics 7: e1001291.
38. Simpson SJ, Sword GA, Lo N, (2011) Polyphenism in insects. Curr Biol 21: R738-749.
39. Pener MP, Simpson SJ, (2009) Locust phase polyphenism: an update. Advances in Insect Physiology 36: 1-272.
40. Ma Z, Guo W, Guo X, Wang X, Kang L, (2011) Modulation of behavioral phase changes of the migratory locust by the catecholamine metabolic pathway. Proc Natl Acad Sci U S A 108: 3882-3887.
41. Wei Y, Chen S, Yang P, Ma Z, Kang L, (2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 10: R6.
42. Malik HS, Eickbush TH, (1998) The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol Biol Evol 15: 1123-1134.
43. Raghavan N, Tettelin H, Miller A, Hostetler J, Tallon L, et al. (2007) Nimbus (BgI): an active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata. Int J Parasitol 37: 1307-1318.
44. Kapitonov VV, Tempel S, Jurka J, (2009) Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene 448: 207-213.
45. 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.
46. Schon I, Arkhipova IR, (2006) Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni. Gene 371: 296-307.
47. Tay WT, Behere GT, Batterham P, Heckel DG, (2010) Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes. BMC Evol Biol 10: 144.
48. Rho M, Schaack S, Gao X, Kim S, Lynch M, et al. (2010) LTR retroelements in the genome of Daphnia pulex. BMC Genomics 11: 425.
49. Tubio JM, Naveira H, Costas J, (2005) Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol 22: 29-39.
50. Blumenstiel JP, (2011) Evolutionary dynamics of transposable elements in a small RNA world. Trends Genet 27: 23-31.
51. Han JS, (2010) Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions. Mob DNA 1: 15.
52. Han JS, Szak ST, Boeke JD, (2004) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429: 268-274.
53. Chen S, Yang P, Jiang F, Wei Y, Ma Z, et al. (2010) De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One 5: e15633.
54. Fernandez-Medina RD, Struchiner CJ, Ribeiro JM, (2011) Novel transposable elements from Anopheles gambiae. BMC Genomics 12: 260.
55. Zhao F, Qi J, Schuster SC, (2009) Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. Genome Res 19: 1384-1392.
56. Eickbush TH, Furano AV, (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12: 669-674.
57. Glastad KM, Hunt BG, Yi SV, Goodisman MA, (2011) DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol 20: 553-565.
58. Robinson KL, Tohidi-Esfahani D, Lo N, Simpson SJ, Sword GA, (2011) Evidence for Widespread Genomic Methylation in the Migratory Locust, Locusta migratoria (Orthoptera: Acrididae). PLoS One 6: e28167.
59. Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, et al. (2009) L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev 23: 1303-1312.
60. Oswald J, Engemann S, Lane N, Mayer W, Olek A, et al. (2000) Active demethylation of the paternal genome in the mouse zygote. Curr Biol 10: 475-478.
61. Kang L, Chen X, Zhou Y, Liu B, Zheng W, et al. (2004) The analysis of large-scale gene expression correlated to the phase changes of the migratory locust. Proc Natl Acad Sci U S A 101: 17611-17615.
62. Surget-Groba Y, Montoya-Burgos JI, (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20: 1432-1440.
63. Martin J, Bruno VM, Fang Z, Meng X, Blow M, et al. (2010) Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 11: 663.
64. Robertson G, Schein J, Chiu R, Corbett R, Field M, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7: 909-912.
65. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics 25: 2872-2877.
66. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
67. Huang Y, Niu B, Gao Y, Fu L, Li W, (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
68. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, et al. (2007) Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 8: R127.
69. Sela N, Kim E, Ast G, (2010) The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol 11: R59.
70. Finn RD, Clements J, Eddy SR, (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-37.
71. Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
72. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
73. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) ClustalW and ClustalX version 2.0. Bioinformatics 23: 2947-2948.
74. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
75. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
76. Robinson MD, Oshlack A, (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
77. Pons J, Vogler AP, (2005) Complex pattern of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles. Mol Biol Evol 22: 991-1000.