Identification and evolution of the silkworm helitrons and their contribution to transcripts

DNA Research

Volumn 20, Issue 5, 2013, Pages 471-484

  Han, Min Jin ^a   Shen, Yi Hong ^a   Xu, Meng Shu ^a   Liang, Hong Yu ^a   Zhang, Hua Hao ^b   Zhang, Ze ^b  

^a SOUTHWEST UNIVERSITY   (China)

^b CHONGQING UNIVERSITY   (China)

Author keywords

Evolution; Gene fragment acquisition; Helitron; Silkworm; Transcript

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BOMBYX MORI; CONSENSUS SEQUENCE; EVOLUTION; GENE IDENTIFICATION; GENE INSERTION; GENE SEQUENCE; GENETIC VARIABILITY; HELITRONS; INSECT GENOME; NONHUMAN; POLYMERASE CHAIN REACTION; TRANSPOSON;

EVOLUTION; GENE FRAGMENT ACQUISITION; HELITRON; SILKWORM; TRANSCRIPT;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BOMBYX; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; GENES, INSECT; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84885086234     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst024     Document Type: Article

References (52)

1. Kapitonov, V.V. and Jurka, J. 2001, Rolling-circle transposons in eukaryotes, Proc. Natl. Acad. Sci. USA, 98, 8714-19.
2. Mendiola, M.V., Bernales, I. and de la Cruz, F. 1994, Differential roles of the transposon termini in IS91 transposition, Proc. Natl. Acad. Sci. USA, 91, 1922-26.
3. Kapitonov, V.V. 2006, Helitron-N1-XT, a family of non-autonomous Helitron from frog, Repbase Reports, 6, 494-6.
4. Putnam, N.H., Srivastava, M., Hellsten, U., et al. 2007, Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization, Science, 317, 86-94.
5. Galagan, J.E., Calvo, S.E., Cuomo, C., et al.2005, Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae, Nature, 438, 1105-15.
6. Pritham, E.J. and Feschotte, C. 2007, Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus, Proc. Natl Acad. Sci. USA, 104, 1895-900.
7. Du, C., Fefelova, N., Caronna, J., He, L. and Dooner, H.K. 2009, The polychromatic Helitron landscape of themaize genome, Proc. Natl Acad. Sci. USA, 106, 19916-21.
8. Yang, L. and Bennetzen, J.L. 2009, Distribution, diversity, evolution, and survival of Helitrons in the maize genome, Proc. Natl Acad. Sci. USA, 106, 19922-7.
9. Kapitonov, V.V. and Jurka, J. 2007, Helitrons in fruit flies, Repbase Reports, 7, 127-32.
10. Zuccolo, A., Sebastian, A., Talag, J., et al. 2007, Transposable element distribution, abundance and role in genome size variation in the genus Oryza, BMC Evol. Biol., 7, 152.
11. Yang, L.andBennetzen, J.L.2009,Structure-baseddiscovery and description of plant and animal Helitrons, Proc. Natl Acad. Sci. USA, 106, 12832-7.
12. Barbaglia, A.M., Klusman, K.M., Higgins, J., Shaw, J.R., Hannah, L.C. and Lal, S.K. 2012, Gene capture by Helitron transposons reshuffles the transcriptome of maize, Genetics, 190, 965-75.
13. Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A. and Rafalski, A. 2005, Gene duplication and exon shuffling by Helitron-like transposons generate intraspecies diversity in maize, Nat. Genet., 37, 997-1002.
14. Xia, Q., Zhou, Z., Lu, C., et al. 2004,A draft sequence for the genome of the domesticated silkworm (Bombyx mori), Science, 306, 1937-40.
15. Zhan, S., Merlin, C., Boore, J.L. and Reppert, S.M. 2011, The monarch butterfly genome yields insights into longdistance migration, Cell, 147, 1171-85.
16. Consortium, T.H.G. 2012, Butterfly genome reveals promiscuous exchange of mimicry adaptations among species, Nature, 487, 94-8.
17. Grimaldi, D. and Engel, M.S. 2005, Evolution of the insects. Cambridge University Press: New York.
18. Osanai-Futahashi, M., Suetsugu, Y., Mita, K. and Fujiwara, H. 2008, Genome-wide screening and characterization of transposableelementsandtheir distribution analysis in the silkworm, Bombyx mori, Insect. Biochem. Mol. Biol., 38, 1046-57.
19. Edgar, R.C. 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460-1.
20. Edgar, R.C. 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792-7.
21. Xia, X. and Xie, Z. 2001,DAMBE: software package for data analysis in molecular biology and evolution, J. Hered., 92, 371-3.
22. Markham, N.R. and Zuker, M. 2008, UNAFold: software for nucleic acid folding and hybridization, Methods Mol. Biol., 453, 3-31.
23. Siguier, P., Perochon, J., Lestrade, L., Mahillon, J. and Chandler, M. 2006, ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Res., 34, D32-6.
24. Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O. and Walichiewicz, J. 2005, Repbase Update, a database of eukaryotic repetitive elements, Cytogenet. Genome Res., 110, 462-7.
25. Nagaraja, G.M. and Nagaraju, J. 1995, Genome fingerprinting of the silkworm, Bombyx mori, using random arbitrary primers, Electrophoresis, 16, 1633-8.
26. Kimura, M. 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences, J. Mol. Evol., 16, 111-20.
27. Li, W.-H. 1997, Molecular evolution. Sinauer Associates: Sunderland, Massachusetts.
28. Xia, Q., Guo, Y., Zhang, Z., et al. 2009, Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx), Science, 326, 433-6.
29. Tamura, K., Dudley, J., Nei, M. and Kumar, S. 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. Evol., 24, 1596-9.
30. Excoffier, L., Laval, G. and Schneider, S. 2005, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinform. Online, 1, 47-50.
31. Duan, J., Li, R., Cheng, D., et al. 2010, SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology, Nucleic Acids Res., 38, 453-6.
32. Han, M.J., Shen, Y.H., Gao, Y.H., Chen, L.Y., Xiang, Z.H. and Zhang, Z. 2010, Burst expansion, distribution and diversification of MITEs in the silkworm genome, BMC genomics, 11, 520.
33. Thomas, J., Schaack, S. and Pritham, E.J. 2010, Pervasive horizontal transfer of rolling-circle transposons among animals, Genome Biol. Evol., 2, 656-64.
34. Coates, B.S., Hellmich, R.L., Grant, D.M. and Abel, C.A. 2012, Mobilizing the genome of Lepidoptera through novel sequence gains and end creation by non-autonomous Lep1 Helitrons, DNA Res., 19, 11-21.
35. Zerjal, T., Joets, J., Alix, K., Grandbastien, M.A. and Tenaillon, M.I. 2009, Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome, Plant Mol. Biol., 71, 99-114.
36. Rogers, A.R. and Harpending, H. 1992, Population growth makeswaves inthe distribution ofpairwise genetic differences, Mol. Biol. Evol., 9, 552-69.
37. Sweredoski, M., DeRose-Wilson, L. and Gaut, B.S. 2008, A comparative computational analysis of nonautonomous Helitron elements betweenmaizeandrice, BMCgenomics, 9, 467.
38. Coates, B.S., Sumerford, D.V., Hellmich, R.L. and Lewis, L.C. 2010, A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family, J. Mol. Evol., 70, 275-88.
39. Smit, A.F.A. 2006, Repeat Masker edition, Release 20061006, Repbase Update.
40. Hollister, J.D. and Gaut, B.S. 2007, Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana, Mol. Biol. Evol, 24, 2515-24.
41. Yang, G., Nagel, D.H., Feschotte, C., Hancock, C.N. and Wessler, S.R. 2009, Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE, Science, 325, 1391-4.
42. Jiang, N., Bao, Z., Zhang, X., et al. 2003, An active DNA transposon family in rice, Nature, 421, 163-7.
43. Nakazaki, T., Okumoto, Y., Horibata, A., et al. 2003, Mobilization of a transposon in the rice genome, Nature, 421, 170-2.
44. Naito, K., Cho, E., Yang, G.J., et al. 2006, Dramatic amplification of a rice transposable element during recent domestication, Proc. Natl Acad. Sci. USA, 103, 17620-5.
45. Yoshitake, N. 1968, Phylogenetic aspects on the origin of Japanese race of the silkworm, Bombyx mori L, J. Sericol. Sci. Jpn, 37, 83-7.
46. Sun, W., Yu, H., Shen, Y., Banno, Y., Xiang, Z. and Zhang, Z. 2012, Phylogeny and evolutionary history of the silkworm, Sci. China Life Sci., 55, 483-96.
47. Feschotte, C. and Pritham, E.J. 2009, A cornucopia of Helitrons shapes the maize genome, Proc. Natl. Acad. Sci. USA, 106, 19747-8.
48. Feschotte, C.andWessler, S.R.2001,Treasures in theattic: rolling circle transposons discovered in eukaryotic genomes, Proc. Natl Acad. Sci. USA, 98, 8923-4.
49. Bennetzen, J.L. 2005, Transposable elements, gene creation and genome rearrangement in flowering plants, Curr. Opin. Genet. Dev., 15, 621-7.
50. Brunner, S., Pea, G. and Rafalski, A. 2005, Origins, genetic organization and transcription of a family of nonautonomous Helitron elements in maize, Plant J., 43, 799-810.
51. Lal, S., Oetjens, M. and Hannah, L.C. 2009, Helitrons: Enigmatic abductors and mobilizers of host genome sequences, Plant Sci., 176, 181-6.
52. Dong, Y., Lu, X., Song, W., et al. 2011, Structural characterization of Helitrons and their stepwise capturing of gene fragments in the maize genome, BMC Genomics, 12, 609.