A Novel Family of Terminal-Repeat Retrotransposon in Miniature (TRIM) in the Genome of the Red Harvester Ant, Pogonomyrmex barbatus

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Zhou, Yihong ^a   Cahan, Sara Helms ^a  

^a UNIVERSITY OF VERMONT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANT; ARTICLE; GENE DUPLICATION; GENE SEQUENCE; INSECT GENOME; LONG TERMINAL REPEAT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RED HARVESTER ANT; RETROPOSON; SEQUENCE HOMOLOGY; TERMINAL REPEAT RETROTRANSPOSON IN MINIATURE;

ANIMALS; ANTS; BASE SEQUENCE; CHROMOSOME MAPPING; GENOME, INSECT; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, INSERTIONAL; PHYLOGENY; RETROELEMENTS; SEQUENCE HOMOLOGY; TERMINAL REPEAT SEQUENCES;

HYMENOPTERA; MYRMICINAE; POGONOMYRMEX BARBATUS;

EID: 84871704864     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053401     Document Type: Article

References (49)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
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. Wessler SR, (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci USA 103: 17600-17601.
5. Kumar A, Bennetzen JL, (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
6. Neumann P, Pozarkova D, Macas J, (2003) Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol Biol 53: 399-410.
7. McCollum AM, Ganko EW, Barrass PA, Rodriguez JM, McDonald JF, (2002) Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. BMC Evol Biol 2: 5-12.
8. Gao D, Chen JF, Chen JF, Chen MS, Meyers BC, et al. (2012) A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS ONE 7: e32010 doi:10.1371/journal.pone.0032010.
9. Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, et al. (2004) Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166: 1437-1450.
10. Witte CP, Le QH, Bureau T, Kumar A, (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA 98: 13778-13783.
11. Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, et al. (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA 105: 5833-5838.
12. Nakatsuka T, Nishihara M, Mishiba K, Hirano H, Yamamura S, (2006) Two different transposable elements inserted in flavonoid 3′, 5′-hydroxylase gene contribute to pink flower coloration in Gentiana scabra. Mol Gen Genomics 275: 231-241.
13. Kwon SJ, Kim DH, Lim MH, Long Y, Meng JL, et al. (2007) Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genomics 278: 361-370.
14. Yang TJ, Kwon SJ, Choi BS, Kim JS, Jin M, et al. (2007) Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theor Appl Genet 114: 627-636.
15. Taber SW (1998) The world of the harvester ants, Texas A&M University Press, College Station, TX.
16. Helms Cahan S, Parker JD, Rissing SW, Johnson RA, Polony TS, et al. (2002) Extreme genetic differences between queens and workers in hybridizing Pogonomyrmex harvester ants. Proc R Soc Lond Ser B 269: 1871-1877.
17. Julian GE, Fewell JH, Gadau J, Johnson RA, Larrabee D, (2002) Genetic determination of the queen caste in an ant hybrid zone. Proc Natl Acad Sci USA 99: 8157-8160.
18. Charlesworth B, Sniegowski P, Stephan W, (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
19. Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, et al. (2011) Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci USA 108: 5667-5672.
20. Gadau J, Helmkampf M, Nygaard S, Roux J, Simola DF, et al. (2012) The genomic impact of 100 million years of social evolution in seven ant species. Trends Genet 28: 14-21.
21. Temin HM, (1981) Structure, variation and synthesis of retrovirus long terminal repeat. Cell 27: 1-3.
22. Xu Z, Wang H, (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: 265-268.
23. Bender J, Kleckner N, (1992) Tn10 insertion specificity is strongly dependent upon sequences immediately adjacent to the target-site consensus sequence. Proc Natl Acad Sci USA 89: 7996-8000.
24. Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, et al. (2009) Fourmidable: a database for ant genomics. BMC Genomics 10: 5-10.
25. Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, et al. (2011) Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Res 39 (suppl 1) (): D658-D662 doi:10.1093/nar/gkq1145.
26. Maddison DR, Maddison WP (2003) MacClade 4: Analysis of phylogeny and character evolution, Version 4.06, Sinauer Associates, Sunderland, Massachusetts.
27. Kalendar R, Antonius K, Smýkal P, Schulman AH, (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121: 1419-1430.
28. LeGrice SFJ, (2003) "In the beginning": initiation of minus strand DNA synthesis in retroviruses and LTR-containing retrotransposons. Biochemistry 42: 14349-14355.
29. Levin HL, Moran JV, (2011) Dynamic interactions between transposable elements and their hosts. Nature reviews 12: 615-627.
30. Williamson VM, (1983) Transposable elements in yeast. Int Rev Cytol 83: 1-25.
31. Bennetzen JL, (2000) Transposable element contributions to plant gene and genome evolution. J Plant Biol 42: 251-269.
32. Lim JK, Simmons MJ, (1994) Gross chromosome rearrangements mediated by transposable elements in Drosophila. BioEssays 16: 269-275.
33. Bennetzen JL, Kellog EA, (1997) Do plants have a one-way tickets to genomic obesity? Plant Cell 9: 1509-1514.
34. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, et al. (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 3: RESEARCH0084.
35. Linheiro RS, Bergman CM, (2012) Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS ONE 7: e30008 doi:10.1371/journal.pone.0030008.
36. Vigdal TJ, Kaufman CD, Izsvak Z, Voytas DF, Ivics Z, (2002) Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements. J Mol Biol 323: 441-452.
37. Nefedova LN, Mannanova MM, Kim AI, (2011) Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome. Virus Genes 42: 297-306.
38. Bowen NJ, Jordan IK, Epstein JA, Wood V, Levin HL, (2003) Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res 13: 1984-1997.
39. Majumdar A, Chatterjee AG, Ripmaster TL, Levin HL, (2011) Determinants that specify the integration pattern of retrotransposon Tf1 in the fbp1 promoter of Schizosaccharomyces pombe. J Virol 85: 519-529.
40. Chalker DL, Sandmeyer SB, (1992) Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 6: 117-128.
41. Zhu Y, Dai J, Fuers PG, Voytas DF, (2003) Controlling integration specificity of a yeast retrotransposon. Proc Natl Acad Sci USA 100: 5891-5895.
42. Moreau CS, Bell CD, Vila R, Achibald SB, Pierce NE, (2006) Phylogeny of the ants: diversification in the age of angiosperms. Science 312: 101-104.
43. Brady SG, Fisher BL, Ward PS, (2006) Evaluating alternative hypotheses for the early evolution and diversification of ants. Proc Natl Acad Sci USA 103: 18172-18177.
44. Loreto ELS, Carareto CMA, Capy P, (2008) Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 100: 545-554.
45. Keeling PJ, Palmer JD, (2008) Horizontal gene transfer in eukaryotic evolution. Nature Rev Genet 9: 605-618.
46. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, et al. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-767.
47. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
48. Li W (1997) Molecular Evolution, Sinauer Associates, Sunderland, MA.
49. Helms Cahan S, Julian GE, Schwander T, Keller L, (2006) Reproductive isolation between Pogonomyrmex rugosus and two lineages with genetic caste determination. Ecology 87: 2160-2170.