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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.
J Integr Plant Biol 2008; 50(9):1130-9JI

Abstract

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 (approximately 5,000) and Ty3-gypsy (approximately 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.

Authors+Show Affiliations

College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang 110161, China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

18844781

Citation

Sun, Hai-Yue, 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, vol. 50, no. 9, 2008, pp. 1130-9.
Sun HY, Dai HY, Zhao GL, 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 Integr Plant Biol. 2008;50(9):1130-9.
Sun, H. Y., Dai, H. Y., Zhao, G. L., Ma, Y., Ou, C. Q., Li, H., ... Zhang, Z. H. (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), pp. 1130-9. doi:10.1111/j.1744-7909.2008.00717.x.
Sun HY, 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 Integr Plant Biol. 2008;50(9):1130-9. PubMed PMID: 18844781.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Sun,Hai-Yue, AU - Dai,Hong-Yan, AU - Zhao,Gui-Ling, AU - Ma,Yue, AU - Ou,Chun-Qing, AU - Li,He, AU - Li,Lin-Guang, AU - Zhang,Zhi-Hong, PY - 2008/10/11/pubmed PY - 2009/1/24/medline PY - 2008/10/11/entrez SP - 1130 EP - 9 JF - Journal of integrative plant biology JO - J Integr Plant Biol VL - 50 IS - 9 N2 - 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 (approximately 5,000) and Ty3-gypsy (approximately 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. SN - 1744-7909 UR - https://www.unboundmedicine.com/medline/citation/18844781/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_ L2 - https://doi.org/10.1111/j.1744-7909.2008.00717.x DB - PRIME DP - Unbound Medicine ER -