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  

作　　者：Hai-Yue Sun Hong-Yan Dai Gui-Ling Zhao Yue Ma Chun-Qing Ou He Li Lin-Guang Li Zhi-Hong Zhang 

机构地区：[1]College of Horticulture, Shenyang Agriculturel University, Dongling Road 120, S henyang 110161, China [2]College of Forestry, Shenyang Agricultural University, Dongling Road 120, Shenyang 110161, China [3]Shandong Institute of Pomology, Longtan Road 64, Tai'an 271000, China

出　　处：《Journal of Integrative Plant Biology》2008年第9期1130-1139,共10页植物学报（英文版）

基　　金：the National Natural Science Foundation of China (30500348);Specialized Research Fund for the Doctoral Program of Higher Education(20050157003)

摘　　要：The conserved domains of reverse transcriptase （RT） genes of Tyl-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 （-5000） and Ty3-gypsy （-26000）. 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 Tyl.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.The conserved domains of reverse transcriptase （RT） genes of Tyl-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 （-5000） and Ty3-gypsy （-26000）. 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 Tyl.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：HETEROGENEITY Malusdomestica RETROTRANSPOSON reverse transcriptase transcriptional activity 

分 类 号：Q753[生物学—分子生物学] Q55