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

Molecular Genetics and Genomics

Volumn 272, Issue 1, 2004, Pages 116-127

  Tahara, M ^a   Aoki, T ^b   Suzuka, S ^c   Yamashita, H ^a   Tanaka, M ^d   Matsunaga, S ^e   Kokumai, S ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b JEOL LTD   (Japan)

^c SK Foods   (Japan)

^d NATIONAL AGRICULTURAL RESEARCH CENTER FOR KYUSHU OKINAWA REGION   (Japan)

^e Kabaya Foods   (Japan)

Author keywords

Ipomoea batatas; Retrotransposon; Sequence specific amplification polymorphism (S SAP); Transposition

Indexed keywords

COMPLEMENTARY DNA; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; DNA POLYMORPHISM; DNA RESPONSIVE ELEMENT; DNA TRANSPOSITION; GENE AMPLIFICATION; GENE IDENTIFICATION; GENOME; GENOME ANALYSIS; GENOMICS; LONG TERMINAL REPEAT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CELL CULTURE; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN DETERMINATION; RETROPOSON; SEQUENCE ANALYSIS; SWEET POTATO;

BASE SEQUENCE; GENE DOSAGE; IPOMOEA BATATAS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RETROELEMENTS;

INSERTION SEQUENCES; IPOMOEA; IPOMOEA BATATAS;

EID: 4544229957     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-004-1044-2     Document Type: Article

References (34)

1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218
2. 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
3. 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
4. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 38:783-791
5. 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
6. Grandbastien MA (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181-187
7. 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
8. 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
9. Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12:2521-2528
10. Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118-122
11. Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233:209-216
12. 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
13. 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
14. 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
15. Johns MA, Mottinger J, Freeling M (1985) A low copy number, copia -like transposon in maize. EMBO J 8:1093-1102
16. 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
17. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479-532
18. 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
19. 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
20. 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
21. Li Q, Hunt AG (1997) The polyadenylation of RNA in plants. Plant Physiol 115:321-325
22. Manninen I, Schulman AH (1993) BARE-1, a copia -like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22:829-846
23. 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
24. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:474-497
25. Preston BD (1996) Error-prone retrotransposition: rime of the ancient mutators. Proc Natl Acad Sci USA 93:7427-7431
26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. 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
34. 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