LTR-retrotransposon diversity and transcriptional activation under phytoplasma stress in Ziziphus jujuba

详细信息    查看全文

• 作者：Jun Sun (1)
  Yao Huang (1)
  Junyong Zhou (2)
  Jing Guo (1)
  Qibao Sun (2)
  
• 关键词：Jujube ; Long terminal repeat retrotransposons ; Heterogeneity ; gypsy ; copia ; Diversity
• 刊名：Tree Genetics & Genomes
• 出版年：2013
• 出版时间：April 2013
• 年：2013
• 卷：9
• 期：2
• 页码：423-431
• 全文大小：1413KB
• 参考文献：1. Beguiristain T, Grandbastien MA, Puigdomenech P, Casacuberta JM (2001) Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol 127(1):212鈥?21 CrossRef
  2. Casacuberta JM, Santiago N (2003) Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1鈥?1 CrossRef
  3. Casacuberta JM, Vernhettes S, Grandbastien MA (1995) Sequence variability within the tobacco retrotransposon / Tnt1 population. EMBO J 14(11):2670鈥?678
  4. Dixit A, Ma KH, Yu JW, Cho EG, Park YJ (2006) Reverse transcriptase domain sequences from Mungbean ( / Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis. Plant Cell Rep 25(2):100鈥?11 CrossRef
  5. Du XY, Zhang QL, Luo ZR (2009) Development of retrotransposon primers and their utilization for germplasm identification in / Diospyros spp. (Ebenaceae). Tree Genet Genomes 5:235鈥?45 CrossRef
  6. Hansen CN, Heslop-Harrison JS (2004) Sequences and phylogenies of plant pararetroviruses, viruses and transposable elements. Adv Bot Res 41:165鈥?93 CrossRef
  7. Hill P, Burford D, Martin DMA, Flavell AJ (2005) Retrotransposon populations of / Vicia species with varying genome size. Mol Genet Genomics 273(5):371鈥?81 CrossRef
  8. Jeung JU, Cho SK, Lee SJ, Shin JS (2005) Characterization of / Ty3-gypsy-like elements in / Hibiscus syriacus. Mol Cells 19(3):318鈥?27
  9. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley ( / Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci U S A 97(12):6603鈥?607 CrossRef
  10. Kimura Y, Tosa Y, Shimada S, Sogo R, Kusaba M, Sunaga T, Betsuyaku S, Eto Y, Nakayashiki HI, Mayama S (2001) OARE-1, a / Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol 42(12):1345鈥?354 CrossRef
  11. Kumar A (1996) The adventures of the / Ty1-copia group of retrotransposons in plants. Trends Genet 12(2):41鈥?3 CrossRef
  12. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479鈥?32 CrossRef
  13. Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R, Flavell AJ (1997) The / Ty1-copia group of retrotransposons in plants: genomic organisation, evolution and use as molecular markers. Genetica 100:205鈥?17 CrossRef
  14. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5(2):150鈥?63 CrossRef
  15. Kumekawa N, Ohtsubo E, Ohtsubo H (1999) Identification and phylogenetic analysis of / gypsy-type retrotransposons in the plant kingdom. Genes Genet Syst 74(6):299鈥?07 CrossRef
  16. Ma Y, Sun HY, Zhao GL, Dai HY, Gao XY, Li H, Zhang ZH (2008) Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry ( / Fragaria 脳 / ananassa Duch.). Plant Cell Rep 27(3):499鈥?07 CrossRef
  17. Mansour A (2008) Utilization of genomic retrotransposons as cladistic markers. J Cell Mol Biol 7(1):17鈥?8
  18. Matsuoka Y, Tsunewaki K (1999) Evolutionary dynamics of / Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis. Mol Biol Evol 16(2):208鈥?17 CrossRef
  19. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 19:4321鈥?325 CrossRef
  20. Muthukumar B, Bennetzen JL (2004) Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol Genet Genomics 271(3):308鈥?16 CrossRef
  21. Park JM, Schneeweiss GM, Weiss-Schneeweiss H (2007) Diversity and evolution of / Ty1-copia and / Ty3-gypsy retroelements in the non-photosynthetic flowering plants / Orobanche and / Phelipanche (Orobanchaceae). Gene 387:75鈥?6 CrossRef
  22. Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genomics 271(1):91鈥?7 CrossRef
  23. Ramallo E, Kalendar R, Schulman AH, Mart铆nez-Izquierdo JA (2008) / Reme1, a / Copia retrotransposon in melon, is transcriptionally induced by UV light. Plant Mol Biol 66:137鈥?50 CrossRef
  24. Rico-Cabanas L, Mart铆nez-Izquierdo JA (2007) CIRE1, a novel transcriptionally active / Ty1-copia retrotransposon from / Citrus sinensis. Mol Genet Genomics 277(4):365鈥?77 CrossRef
  25. SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot 82:37鈥?4 CrossRef
  26. Shi CY, Wan XC, Jiang CJ, Sun J (2007) Method for high-quality total RNA isolation from tea plant ( / Camellia sinensis L.). J Anhui Agric Univ 34:360鈥?63
  27. Su PY, Brown TA (1997) Ty3/gypsy-like retrotransposon sequences in tomato. Plasmid 38(3):148鈥?57 CrossRef
  28. Sun J, Fang JG, Wang F, Sun QB, Zhang Z (2010) Characterization of RNaseH-LTR sections of Ty1-copia retrotransposons and fingerprinting of clones by S-SAP analysis in apple. J Hortic Sci Biotechnol 85(1):53鈥?8
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876鈥?882 CrossRef
  30. Vernhettes S, Grandbastien MA, Casacuberta JM (1997) In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Mol Biol 35(5):673鈥?79 CrossRef
  31. Vitte C, Panaud O (2005) LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 110:91鈥?07 CrossRef
  32. Wang HN, Wu YF, An FQ, Gu PW, Zhang ZL (2007) The homology analysis for sequences of 16S rDNA and / tuf gene of phytoplasma from jujube witches鈥?broom and wild jujube witches鈥?broom. SciAgricu Sin 40(10):2200鈥?205
  33. Zhao J, Liu MJ, Dai L, Zhao JY (2006) The variations of endogenous hormones in Chinese jujube infected with witches鈥?broom disease. SciAgricu Sin 39(11):2255鈥?260
  
• 作者单位：Jun Sun (1)
  Yao Huang (1)
  Junyong Zhou (2)
  Jing Guo (1)
  Qibao Sun (2)
  
  1. College of Horticulture, Anhui Agricultural University, 130 West Changjiang Road, Hefei City, 230036, Anhui Province, People鈥檚 Republic of China
  2. Horticulture of Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei City, 230031, Anhui Province, People鈥檚 Republic of China
  

文摘

Degenerate primers were used to amplify the conserved domains of the Ty1-copia and Ty3-gypsy reverse transcriptase (RT) genes of the long terminal repeat retrotransposons in the jujube (Ziziphus jujuba Mill.) genome. Sequence analysis showed that 18 of the 50 Ty1-copia unique sequences and 28 of the 38 Ty3-gypsy unique sequences possessed stop codons, frameshifts, or both. The overall sequence divergence in jujube was higher in the Ty3-gypsy than the Ty1-copia group, in contrast to the results from other plants. Our results showed that sequence heterogeneity during vertical transmission could be a major influence on the evolution of copia- and gypsy-type retroelements in the jujube genome. In order to elucidate the transcriptional activity under phytoplasma stress of these two classes of RTs, RT-PCR primers were designed to amplify products corresponding to either the Ty3-gypsy or Ty1-copia RT domains from total RNA extracted from leaves or flowers of plants infected by phytoplasma. Amplification products were present for Ty3-gypsy RT in both tissues during infection; however, no RT-PCR products were amplified using the Ty1-copia RT domain primers in phytoplasma-infected leaves or flowers. RT-PCR amplification from total RNA extracted from leaves or flowers of healthy plants did not yield either of the RT fragments. The Ty3-gypsy RT-PCR products were confirmed to originate from the Z. jujuba genome. Our results indicated that the gypsy group of retrotransposons was autonomous retroelements. This is the first report characterizing the Ty1-copia and Ty3-gypsy groups of retrotransposons in the Z. jujuba genome.