title: Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.).
abstract: We cloned and characterized Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.). Genomic DNA or methyl jasmonate (MJA)-treated cDNA were used as templates to amplify the reverse transcriptase region of Ty1-copia group retrotransposons. About 280 bp fragments were amplified and cloned, and 97 clones were sequenced. Forty-nine clones included frameshift or the stop codon, or both. Among 48 clones containing complete reading frames, 42 clones had unique nucleotide sequences. Alignment and phylogenetic analysis of putative amino acid sequences in the 42 clones indicated that these clones (named Tdk; retroTransposon in Diospyros kaki) fell into seven subgroups and six ungrouped sequences, indicating high sequence heterogeneity in Tdk clones. Phylogenetic analysis comparing unrelated plant species shows that some Tdk clones are more closely related to Ty1-copia group retrotransposons in the orders Solanales and Sapindales rather than to other Tdk clones. Southern blot analysis using Tdk2B, Tdk4c, Tdk6Ac, Tdk12K and Tdk13G clones as probes showed that persimmon and its related species, D. lotus, D. lotus var. glabba, D. oleifera, D. rhombifolia and D. virginiana, contained multiple Tdk-like sequences, indicating that homologous elements exist in other Diospyros species.
authors.affiliation: Faculty of Life and Environmental Sciences, Shimane University, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Nakatsuka
authors.forename: Naoko
authors.initials: N
authors.lastname: Iwami
authors.forename: Shigehito
authors.initials: S
authors.lastname: Matsumoto
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Itamura
authors.forename: Masumi
authors.initials: M
authors.lastname: Yamagishi
mesh_terms: D000085:Acetates / Q000494:pharmacology; D000595:Amino Acid Sequence; D001483:Base Sequence; D017124:Conserved Sequence; D003517:Cyclopentanes / Q000494:pharmacology; D004251:DNA Transposable Elements / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000032:analysis*; D029788:Diospyros / Q000235:genetics*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D054883:Oxylipins; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000494:pharmacology; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D004251:DNA Transposable Elements; D018076:DNA, Complementary; D018744:DNA, Plant; D054883:Oxylipins; D010937:Plant Growth Regulators; D018626:Retroelements; C072239:methyl jasmonate