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Genome-wide characterization of long terminal repeat-retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons
Alternative TitleGenome-wide Characterization of Long Terminal Repeat -retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons
Sun HaiYue1; Dai HongYan1; Zhao GuiLing1; Ma Yue1; Ou ChunQing1; Li He1; Li LinGuang1; Zhang ZhiHong1
2008
Source PublicationJOURNAL OF INTEGRATIVE PLANT BIOLOGY
ISSN1672-9072
Volume50Issue:9Pages:1130-1139
AbstractThe conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1-copia and Ty3-gypsy group retrotransposons was observed, but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (similar to 5 000) and Ty3-gypsy (similar to 26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1-copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.
Other AbstractThe conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1-copia and Ty3-gypsy group retrotransposons was observed, but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (~5 000) and Ty3-gypsy (~26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1-copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.
KeywordREVERSE-TRANSCRIPTASE DOMAIN PLANT TRANSPOSABLE ELEMENTS PHYLOGENETIC ANALYSIS LTR RETROTRANSPOSONS SEQUENCE ALIGNMENT METHYL JASMONATE CITRUS-SINENSIS TISSUE-CULTURE GYPSY-TYPE EVOLUTION heterogeneity Malus domestica retrotransposon reverse transcriptase transcriptional activity
Indexed ByCSCD
Language英语
Funding Project[National Natural Science Foundation of China] ; [Specialized Research Fund for the Doctoral Program of Higher Education]
CSCD IDCSCD:3324769
Citation statistics
Cited Times:6[CSCD]   [CSCD Record]
Document Type期刊论文
Identifierhttp://ir.imr.ac.cn/handle/321006/156220
Collection中国科学院金属研究所
Affiliation1.中国科学院金属研究所
2.Shandong Institute Pomol, Tai An 271000, Shandong, Peoples R China
Recommended Citation
GB/T 7714
Sun HaiYue,Dai HongYan,Zhao GuiLing,et al. Genome-wide characterization of long terminal repeat-retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons[J]. JOURNAL OF INTEGRATIVE PLANT BIOLOGY,2008,50(9):1130-1139.
APA Sun HaiYue.,Dai HongYan.,Zhao GuiLing.,Ma Yue.,Ou ChunQing.,...&Zhang ZhiHong.(2008).Genome-wide characterization of long terminal repeat-retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons.JOURNAL OF INTEGRATIVE PLANT BIOLOGY,50(9),1130-1139.
MLA Sun HaiYue,et al."Genome-wide characterization of long terminal repeat-retrotransposons in apple reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons".JOURNAL OF INTEGRATIVE PLANT BIOLOGY 50.9(2008):1130-1139.
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