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

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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
其他题名	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
	Sun HaiYue 1; Dai HongYan 1; Zhao GuiLing 1; Ma Yue 1; Ou ChunQing 1; Li He 1; Li LinGuang 1; Zhang ZhiHong 1
	2008
发表期刊	JOURNAL OF INTEGRATIVE PLANT BIOLOGY
ISSN	1672-9072
卷号	50 期号:9 页码:1130-1139
摘要	The 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.
其他摘要	The 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.
关键词	REVERSE-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
收录类别	CSCD
语种	英语
资助项目	[National Natural Science Foundation of China] ; [Specialized Research Fund for the Doctoral Program of Higher Education]
CSCD记录号	CSCD:3324769
引用统计	被引频次：7[CSCD] [CSCD记录]
文献类型	期刊论文
条目标识符	http://ir.imr.ac.cn/handle/321006/156220
专题	中国科学院金属研究所
作者单位	1.中国科学院金属研究所 2.Shandong Institute Pomol, Tai An 271000, Shandong, Peoples R China
推荐引用方式 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.