Characterization of active miniature inverted-repeat transposable elements in the peanut genome

Theoretical and Applied Genetics

Volumn 124, Issue 8, 2012, Pages 1429-1438

  Shirasawa, Kenta ^a   Hirakawa, Hideki ^a   Tabata, Satoshi ^a   Hasegawa, Makoto ^b   Kiyoshima, Hiroyuki ^b   Suzuki, Sigeru ^b   Sasamoto, Sigemi ^a   Watanabe, Akiko ^a   Fujishiro, Tsunakazu ^a   Isobe, Sachiko ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b Chiba Prefectural Agriculture and Forestry Research Center 1762   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACIDS; GENES; POLYMERASE CHAIN REACTION;

ARACHIS HYPOGAEA; FLANKING SEQUENCE; GENOMIC DIVERSITY; GENOMIC LIBRARIES; MINIATURE INVERTED-REPEAT TRANSPOSABLE ELEMENTS; NONAUTONOMOUS; SOUTHERN BLOT ANALYSIS; TERMINAL INVERTED REPEAT;

OILSEEDS;

ACARI; ANIMALIA; ARACHIS HYPOGAEA;

DNA; PRIMER DNA;

ARTICLE; BIOLOGICAL MODEL; CROSS BREEDING; GENETIC POLYMORPHISM; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PEANUT; PHYLOGENY; PLANT GENE; PLANT GENOME; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; TRANSPOSON;

ARACHIS HYPOGAEA; BASE SEQUENCE; CROSSES, GENETIC; DNA; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; GENES, PLANT; GENOME, PLANT; GENOMICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84865698207     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1798-6     Document Type: Article

References (47)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Bonin A, Paris M, Despres L, Tetreau G, David JP, Kilian A (2008) A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection. BMC Genomics 9: 459.
3. Bureau TE, Wessler SR (1994) Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci USA 91: 1411-1415.
4. Burow MD, Simpson CE, Starr JL, Paterson AH (2001) Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 159: 823-837.
5. Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family Heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci USA 97: 10083-10089.
6. Casacuberta E, Casacuberta JM, Puigdomenech P, Monfort A (1998) Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements. Plant J 16: 79-85.
7. Charrier B, Foucher F, Kondorosi E, d'Aubenton-Carafa Y, Thermes C, Kondorosi A, Ratet P (1999) Bigfoot: a new family of MITE elements characterized from the Medicago genus. Plant J 18: 431-441.
8. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
9. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
10. Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108: 1064-1070.
11. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3: 329-341.
12. Gierl A, Saedler H (1992) Plant-transposable elements and gene tagging. Plant Mol Biol 19: 39-49.
13. Gowda MVC, Bhat RS, Motagi BN, Sujay V, Kumari V, Sujatha B (2010) Association of high-frequency origin of late leaf spot resistant mutants with AhMITE1 transposition in peanut. Plant Breed 129: 567-569.
14. Gowda MVC, Bhat RS, Sujay V, Kusuma P, Varshakumari Bhat S, Varshney RK (2011) Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.). Plant Syst Evol 291: 153-159.
15. Grzebelus D, Gladysz M, Macko-Podgorni A, Gambin T, Golis B, Rakoczy R, Gambin A (2009) Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene 448: 214-220.
16. He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 3: 3.
17. Henikoff S, Till BJ, Comai L (2004) TILLING. Traditional mutagenesis meets functional genomics. Plant Physiol 135: 630-636.
18. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9: 868-877.
19. Huang X, Wang J, Aluru S, Yang SP, Hillier L (2003) PCAP: a whole-genome assembly program. Genome Res 13: 2164-2170.
20. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
21. Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR (2003) An active DNA transposon family in rice. Nature 421: 163-167.
22. Kikuchi K, Terauchi K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170.
23. Knoll JE, Ramos ML, Zeng Y, Holbrook CC, Chow M et al (2011) TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol 11: 81.
24. Kochert G, Stalker HT, Gimenes M, Galagro L, Lopes CR, Moore K (1996) RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot 83: 1282-1291.
25. Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H et al (2011) Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breed. doi: 10. 1007/s11032-011-9604-8.
26. Krapovickas A, Gregory W (1994) Taxonomia del genero Arachis (Leguminosae). Bonplandia 8: 1-186.
27. Krapovickas A, Gregory W (2007) Taxonomy of the genus Arachis (Leguminosae). Bonplandia 16: 1-205.
28. Lin X, Long L, Shan X, Zhang S, Shen S, Liu B (2006) In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization. J Exp Bot 57: 2313-2323.
29. McClintock B (1951) Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 16: 13-47.
30. Momose M, Abe Y, Ozeki Y (2010) Miniature inverted-repeat transposable elements of Stowaway are active in potato. Genetics 186: 59-66.
31. Monden Y, Naito K, Okumoto Y, Saito H, Oki N et al (2009) High potential of a transposon mPing as a marker system in japonica × japonica cross in rice. DNA Res 16: 131-140.
32. Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JF, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4: 11.
33. Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SC et al (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111: 1060-1071.
34. Moretzsohn MC, Barbosa AV, Alves-Freitas DM, Teixeira C, Leal-Bertioli SC et al (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9: 40.
35. Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN et al (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134.
36. Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M et al (2003) Mobilization of a transposon in the rice genome. Nature 421: 170-172.
37. Nielen S, Campos-Fonseca F, Leal-Bertioli S, Guimaraes P, Seijo G et al (2010) FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosom Res 18: 227-246.
38. Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2006) A protocol for the construction of microsatellite enriched genomic library. Plant Mol Bio Rep 24: 305-312.
39. Patel M, Jung S, Moore K, Powell G, Ainsworth C, Abbott A (2004) High-oleate peanut mutants result from a MITE insertion into the FAD2 gene. Theor Appl Genet 108: 1492-1502.
40. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
41. Proite K, Leal-Bertioli SC, Bertioli DJ, Moretzsohn MC, da Silva FR, Martins NF, Guimaraes PM (2007) ESTs from a wild Arachis species for gene discovery and marker development. BMC Plant Biol 7: 7.
42. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
43. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15: 227-239.
44. Shan X, Liu Z, Dong Z, Wang Y, Chen Y et al (2005) Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol Biol Evol 22: 976-990.
45. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
46. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
47. Yüksel B, Paterson AH (2005) Construction and characterization of a peanut HindIII BAC library. Theor Appl Genet 111: 630-639.