Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome

Springer Science and Business Media LLC - Tập 272 Số 1 - Trang 116-127 - 2004
Makoto Tahara1, Takayuki Aoki2, Sandra M. Suzuka3, Hiroki Yamashita1, Masaru Tanaka4, S. Matsunaga5, Shingo KOKUMAI1
1Faculty of Agriculture, Okayama University, 700-8530, Okayama, Okayama, Japan
2JEOL, 196-8558, Akishima, Tokyo, Japan
3SK Foods, 651-2124, Kobe, Hyogo, Japan
4National Agricultural Research Center for Kyushu Okinawa Region, National Agricultural Research Organization, 885-0091, Miyakonojyo, Miyazaki, Japan
5Kabaya Foods, 709-2117, Mitsu, Okayama, Japan

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Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

Beguiristain T, Grandbastien MA, Puigdomenech P, Casacuberta JM (2001) Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol 127:212–221

Clark SE, Williams RW, Meyerowitz EM (1997) The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell 89:575–585

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 38:783–791

Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNA from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA 85:8998–9002

Grandbastien MA (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181–187

Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376–380

Hayakawa T (1997) Methods of DNA and RNA extraction from tobacco ( Nicotiana tabaccum). In: Shimamoto I. Sasaki T (eds.) Protocols of PCR experiments for plants. Shujunsha, Tokyo, pp 45–47

Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12:2521–2528

Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118–122

Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233:209–216

Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788

Ivashuta S, Naumkina M, Gau M, Uchiyama K, Isobe S, Mizukami Y, Shimamoto Y (2002) Genotype-dependent transcriptional activation of novel repetitive elements during cold acclimation of alfalfa ( Medicago sativa). Plant J 31:615–627

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

Johns MA, Mottinger J, Freeling M (1985) A low copy number, copia -like transposon in maize. EMBO J 8:1093–1102

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E (1999) Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol Gen Genet 260:593–602

Lall IPS, Maneesha, Upadhyaya KC (2002) Panzee, a copia -like retrotransposon from the grain legume pigeonpea ( Cajanus cajan L.). Mol Genet Genomics 267:271–280

Laten HM, Majumdar A, Gaucher EA (1998) SIRE-1, a copia/Ty1 -like retroelement from soybean, encodes a retroviral envelope-like protein. Proc Natl Acad Sci USA 95:6897–6902

Li Q, Hunt AG (1997) The polyadenylation of RNA in plants. Plant Physiol 115:321–325

Manninen I, Schulman AH (1993) BARE-1, a copia -like retroelement in barley ( Hordeum vulgare L.). Plant Mol Biol 22:829–846

Melayah D, Bonnivard E, Chalhoub B, Audeon C, Grandbastien MA (2001) The mobility of the tobacco Tnt1 retrotransposon is correlated with its transcriptional activation by fungal factors. Plant J 28:159–168

Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:474–497

Preston BD (1996) Error-prone retrotransposition: rime of the ancient mutators. Proc Natl Acad Sci USA 93:7427–7431

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

Shimonishi K, Fujita E, Kouzuma M, Ichi K, Ikeda K, Torigoe H (2001) Problems in sweetpotato production related to ‘cultivar decline’ in Kagoshima Prefecture. In: Proceedings of International Workshop on Sweetpotato Cultivar Decline Study. Kyushu Natl Agric Exp Station, Miyazaki, Japan, pp. 33–41

Suoniemi A, Narvanto A, Schulman A (1996) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295–306

Takeda S, Sugimoto K, Otsuki H, Hirochika H (1999) A 13-bp cis -regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant J 18:383–393

Tanaka M, Yoshinaga M, Nakazawa Y, Nakatani M (2001) Identification of a novel SINE-like sequence in retrotransposon fragments of sweet potato. Plant Biotechnol 18:157–161

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

Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) copia -like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128

Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

Yamamoto E, Karakaya HC, Knap HT (2000) Molecular characterization of two soybean homologs of Arabidopsis thaliana CLAVATA1 from the wild type and fasciation mutant. Biochim Biophys Acta 1491:333–340