New insights into helitron transposable elements in the mesopolyploid species Brassica rapa

Gene

Volumn 532, Issue 2, 2013, Pages 236-245

  Fu, Donghui ^a   Wei, Lijuan ^b   Xiao, Meili ^b   Hayward, Alice ^c  

^a JIANGXI AGRICULTURAL UNIVERSITY   (China)

^b SOUTHWEST UNIVERSITY   (China)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Brassica; Helitron; MicroRNA; Repetitive sequence; Transposon

Indexed keywords

MICRORNA; PLANT DNA; PLANT RNA;

ARTICLE; BINDING AFFINITY; BRASSICA RAPA; DNA BASE COMPOSITION; GENE CONTROL; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; NONHUMAN; PLANT GENE; PLANT GENOME; PRIORITY JOURNAL; TRANSPOSON;

BRASSICA; HELITRON; LINE; LONG INTERSPERSED ELEMENT; LONG TERMINAL REPEAT; LTR; MICRORNA; MIRNA; PLANT SMALL RNA TARGET ANALYSIS SERVER; PSRNATARGET; RC; REPETITIVE SEQUENCE; REPLICATION PROTEIN A; ROLLING CIRCLE; RPA; SHORT INTERSPERSED ELEMENT; SIMPLE SEQUENCE REPEAT; SINE; SSR; TARGET SITE DUPLICATIONS; TE; TERMINAL INVERTED REPEATS; TIRS; TRANSPOSABLE ELEMENT; TRANSPOSON; TSDS;

BASE COMPOSITION; BASE SEQUENCE; BRASSICA RAPA; CHROMOSOME MAPPING; DNA TRANSPOSABLE ELEMENTS; GENE ONTOLOGY; GENES, PLANT; MICRORNAS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION;

BRASSICA; BRASSICA RAPA; EUKARYOTA;

EID: 84886752591     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.09.033     Document Type: Article

References (50)

1. Brunner S., Pea G., Rafalski A. Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. Plant J. 2005, 43:799-810.
2. Choi J.D., Hoshino A., Park K.I., Park I.S., Iida S. Spontaneous mutations caused by a Helitron transposon, Hel-It1, in morning glory, Ipomoea tricolor. Plant J. 2007, 49:924-934.
3. Coates B.S., Sumerford D.V., Hellmich R.L., Lewis L.C. 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. 2010, 70:275-288.
4. Cocca E., De Iorio S., Capriglione T. Identification of a novel helitron transposon in the genome of Antarctic fish. Mol. Phylogenet. Evol. 2011, 58:439-446.
5. Conesa A., Gotz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 2008:619832.
6. Cultrone A., Dominguez Y.R., Drevet C., Scazzocchio C., Fernandez-Martin R. The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron. Mol. Microbiol. 2007, 63:1577-1587.
7. Da Maia L.C., Palmieri D.A., de Souza V.Q., Kopp M.M., de Carvalho F.I., Costa de Oliveira A. SSR Locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int. J. Plant Genomics 2008, 41.
8. Dai X., Zhao P.X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011, 39:w155-w159.
9. Du C., Caronna J., He L., Dooner H.K. Computational prediction and molecular confirmation of Helitron transposons in the maize genome. BMC Genomics 2008, 9:51.
10. Du C., Fefelova N., Caronna J., He L., Dooner H.K. The polychromatic Helitron landscape of the maize genome. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19916-19921.
11. Eyre-Walker A. Recombination and mammalian genome evolution. Proc. Biol. Sci. 1993, 252:237-243.
12. Feschotte C., Jiang N., Wessler S.R. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 2002, 3:329-341.
13. Fullerton S.M., Bernardo Carvalho A., Clark A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 2001, 18:1139-1142.
14. Gao C., et al. Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species. Mol. Biol. Rep. 2012, 39:7513-7523.
15. Gupta S., Gallavotti A., Stryker G.A., Schmidt R.J., Lal S.K. A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol. Biol. 2005, 57:115-127.
16. Hollister J.D., Gaut B.S. Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol. Biol. Evol. 2007, 24:2515-2524.
17. Hood M.E. Repetitive DNA in the automictic fungus Microbotryum violaceum. Genetica 2005, 124:1-10.
18. Jameson N., Georgelis N., Fouladbash E., Martens S., Hannah L.C., Lal S. Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize. Plant Mol. Biol. 2008, 67:295-304.
19. Jiang N., Ferguson A.A., Slotkin R.K., Lisch D. Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:1537-1542.
20. Kapitonov V.V., Jurka J. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:8714-8719.
21. Kapitonov V.V., Jurka J. Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet. 2007, 23:521-529.
22. Koch M.A., Haubold B., Mitchell-Olds T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera(Brassicaceae). Mol. Biol. Evol. 2000, 17:1483-1498.
23. Kohl M., Wiese S., Warscheid B. Cytoscape: software for visualization and analysis of biological networks. Methods Mol. Biol. 2011, 696:291-303.
24. Lai J., Li Y., Messing J., Dooner H.K. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:9068-9073.
25. Lal S.K., Giroux M.J., Brendel V., Vallejos C.E., Hannah L.C. The maize genome contains a helitron insertion. Plant Cell 2003, 15:381-391.
26. Langdon T., Thomas A., Huang L., Farrar K., King J., Armstead I. Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne. BMC Plant Biol. 2009, 9:70.
27. Li Y., Dooner H.K. Excision of Helitron transposons in maize. Genetics 2009, 182:399-402.
28. Lou P., Wu J., Cheng F., Cressman L.G., Wang X., McClung C.R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell 2012, 24:2415-2426.
29. Madlung A., et al. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 2005, 41:221-230.
30. Morgante M., Brunner S., Pea G., Fengler K., Zuccolo A., Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 2005, 37:997-1002.
31. Mun J.H., et al. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol. 2009, 10:R111.
32. Murad L., et al. The origin and evolution of geminivirus-related DNA sequences in Nicotiana. Heredity 2004, 92:352-358.
33. Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 1935, 389-452.
34. Oliveira E.J., Padua J.G., Zucchi M.I., Vencovsky R., Vieira M.L.C. Origin, evolution and genome distribution of microsatellites. Genet. Mol. Biol. 2006, 29:294-307.
35. Poulter R.T., Goodwin T.J., Butler M.I. Vertebrate helentrons and other novel Helitrons. Gene 2003, 313:201-212.
36. Pritham E.J., Feschotte C. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:1895-1900.
37. Rana D., et al. Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J. 2004, 40:725-733.
38. Rensing S.A., et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 2008, 319:64-69.
39. Smit A.F.A., Hubley R., Green P. RepeatMasker open-3.3.0 (RMLib: 20110419) 1996-2004.
40. Sweredoski M., DeRose-Wilson L., Gaut B.S. A comparative computational analysis of nonautonomous helitron elements between maize and rice. BMC Genomics 2008, 9:467.
41. Town C.D., et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006, 18:1348-1359.
42. Wang Q., Dooner H.K. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:17644-17649.
43. Wang N., et al. Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biol. 2010, 10:190.
44. Wang X., et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43:1035-1039.
45. Xu J.H., Messing J. Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet. 2006, 7:52.
46. Yang L.X., Bennetzen J.L. Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19922-19927.
47. Yang L., Bennetzen J.L. Structure-based discovery and description of plant and animal Helitrons. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:12832-12837.
48. Zabala G., Vodkin L.O. The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell 2005, 17:2619-2632.
49. Zhou Q., et al. Helitron transposons on the sex chromosomes of the platyfish Xiphophorus maculatus and their evolution in animal genomes. Zebrafish 2006, 3:39-52.
50. Zou J., et al. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. Plant J. 2011, 68:212-224.