Advertisement

Plant Molecular Biology Reporter

, Volume 32, Issue 4, pp 923–930 | Cite as

Identification and Characterization of Novel Gypsy-Type Retrotransposons in a Biodiesel Crop, Jatropha curcas L

  • Atefeh Alipour
  • Joyce A. Cartagena
  • Suguru Tsuchimoto
  • Hiroe Sakai
  • Nobuko Ohmido
  • Kiichi Fukui
Brief Communication

Abstract

Gypsy-type retrotransposons comprise a large proportion of the plant genome. Identification and determination of their chromosomal distribution could contribute to a better understanding of the role and dynamics behind the repetitive elements in the genome and karyotype. It would also facilitate the selection of retrotransposon families for informative DNA markers. In the present study, we applied a PCR method by using degenerate oligonucleotide primers to isolate the reverse transcriptase (RT) region of gypsy-type retrotransposons in Jatropha curcas L., a biofuel crop. The analysis of 50 isolated PCR-amplified fragments showed a range of heterogeneity among predicted amino acid sequences. Comparative phylogenetic analyses of isolated RT fragments together with retrotransposon families from other plants allowed us to identify three families (Jg13) of gypsy-type retroelements in the jatropha genome. Jg1 and Jg2, having primer binding sites (PBS) complementary to tRNAArg, were found as jatropha-specific and belonged to the same lineage, which suggests that they arose during early evolution. On the other hand, Jg3 of a different lineage included elements of other species and had PBS complementary to tRNAMet. The computer-based data mining of jatropha whole genome allowed us to identify a high-copy number gypsy-type family Jg4 of the same lineage as Jg1 and Jg2 which had PBS complementary to tRNAArg. Furthermore, fluorescence in situ hybridization (FISH) analysis demonstrated that these gypsy-type elements are located in the pericentromeric region of jatropha chromosomes. The data are discussed within the context of the distinct dynamics of the gypsy-type retrotransposon families, their evolution, and their value for phylogenetic and biodiversity studies.

Keywords

Jatropha curcasGypsy-type retrotransposon Phylogenetic analysis Fluorescence in situ hybridization Biofuel 

Notes

Acknowledgments

The Plant Bioengineering for Bioenergy Laboratory was supported by the SEI-CSR foundation.

Conflict of Interest

The authors declare that they have no conflict of interest.

References

  1. Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K (2013) Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels 6:129PubMedCentralPubMedCrossRefGoogle Scholar
  2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218CrossRefGoogle Scholar
  3. Basha SD, Sujatha M (2007) Inter and intra-population variability of Jatropha curcas (L.) characterized by RAPD and ISSR markers and development of population-specific SCAR markers. Euphytica 156:375–386CrossRefGoogle Scholar
  4. Belyayev A, Raskina O, Nevo E (2001) Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species. Chromosom Res 9:129–136CrossRefGoogle Scholar
  5. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269PubMedCrossRefGoogle Scholar
  6. Domingues D, Cruz GMQ, Metcalfe CJ, Nogueira FTS, Vicentini R, de Alves CS, Van Sluys MA (2012) Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics 13:137PubMedCentralPubMedCrossRefGoogle Scholar
  7. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  8. Feschotte C, Jiang N, Wassler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341PubMedCrossRefGoogle Scholar
  9. Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18:1176–1188PubMedCrossRefGoogle Scholar
  10. Grandbastien MA, Lucas H, Morel JB, Mhiri C, Verbhettes S, Casacuberta JM (1997) The expression of the tobacco Tnt1 retrotransposon is linked to plant defense response. Genetica 100:241–252PubMedCrossRefGoogle Scholar
  11. Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, Kamm A, Doudrick RL, Schwarzacher T, Katsiotis A, Kubis S, Kumar A, Pearce SR, Flavell AJ, Harrison GE (1997) The chromosomal distribution of Ty1-copia group retrotransposable elements in higher plants and their implication for genome evolution. Genetica 100:197–204PubMedCrossRefGoogle Scholar
  12. Hirakawa H, Tsuchimoto S, Sakai H, Nakayama S, Fujishiro T, Kishida Y, Kohara M, Watanabe A, Yamada M, Aizu T, Toyoda A, Fujiyama A, Tabata S, Fukui K, Sato T (2012) Upgraded genomic information of Jatropha curcas L. Plant Biotechnol 29:123–130CrossRefGoogle Scholar
  13. Hribova E, Neumann P, Matsumoto T, Roux N, Macas J, Doležel J (2010) Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biol 10:204PubMedCentralPubMedCrossRefGoogle Scholar
  14. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman A (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 97:6603–6607PubMedCentralPubMedCrossRefGoogle Scholar
  15. Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH (2010) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520–530PubMedCentralPubMedCrossRefGoogle Scholar
  16. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532PubMedCrossRefGoogle Scholar
  17. Kumekawa N, Ohtsubo E, Ohtsubo H (1999) Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom. Genes Genet Syst 74:299–307PubMedCrossRefGoogle Scholar
  18. Muszewska A, Steczkiewicz K, Ginalski K (2013) DIRS and Ngaro retrotransposons in fungi. PloS ONE 8(9):e76319PubMedCentralPubMedCrossRefGoogle Scholar
  19. Ohmido N, Fukui K (1997) Visual verification of close disposition between a rice genomic-specific DNA sequence (TrsA) and the telomere sequence. Plant Mol Biol 35:963–968PubMedCrossRefGoogle Scholar
  20. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  21. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, volume 2, 3rd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
  22. Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-I T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Alipour A, Yuasa S, Matsunaga S, Fukui K (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18:65–76PubMedCentralPubMedCrossRefGoogle Scholar
  23. Sun QB, Li LF, Li Y, Wu GJ, Ge XJ (2008) SSR and AFLP markers reveal low genetic diversity in the biofuel plant Jatropha curcas in China. Crop Sci 48:1865–1871CrossRefGoogle Scholar
  24. Suoniemi A, Tanskanen J, Schulman AH (1998) Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J 13:699–705PubMedCrossRefGoogle Scholar
  25. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  26. Varmus H, Brown P (1989) Retroviruses. In: Berg P, Howe M (eds) Mobile DNA. American Society for Microbiology Press, Washington DC, pp 53–108Google Scholar
  27. Wang CM, Liu P, Yi C, Gu K, Sun F, Li L, Lo LC, Liu X, Feng F, Lin G, Cao S, Hong Y, Yin Z, Yue GH (2011) A first generation microsatellite- and SNP-based linkage map of Jatropha. PloS ONE 6:e23632PubMedCentralPubMedCrossRefGoogle Scholar
  28. Wicker T, Sabot F, Hua-Van A et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982PubMedCrossRefGoogle Scholar
  29. Xu W, Mulpuri S, Liu A (2012) Genetic diversity in the Jatropha genus and its potential application. CAB Rev 7:1–15Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Atefeh Alipour
    • 1
  • Joyce A. Cartagena
    • 2
  • Suguru Tsuchimoto
    • 3
  • Hiroe Sakai
    • 3
  • Nobuko Ohmido
    • 4
  • Kiichi Fukui
    • 1
  1. 1.Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
  2. 2.Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
  3. 3.Plant Bioengineering for Bioenergy Laboratory, Graduate School of EngineeringOsaka UniversitySuitaJapan
  4. 4.Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan

Personalised recommendations