Tree Genetics & Genomes

, Volume 6, Issue 6, pp 941–952 | Cite as

Complete sequence and organisation of the Jatropha curcas (Euphorbiaceae) chloroplast genome

  • Mehar H. Asif
  • Shrikant S. Mantri
  • Ayush Sharma
  • Anukool Srivastava
  • Ila Trivedi
  • Priya Gupta
  • Chandra S. Mohanty
  • Samir V. Sawant
  • Rakesh Tuli
Original Paper

Abstract

Jatropha curcas is an important non-edible oil seed tree species and is considered a promising source of biodiesel. The complete nucleotide sequence of J. curcas chloroplast genome (cpDNA) was determined by pyrosequencing and gaps filled by Sanger sequencing. The cpDNA is a circular molecule of 163,856 bp in length and codes for 110 distinct genes (78 protein coding, four rRNA and 28 distinct tRNA). Genome organisation and arrangement are similar to the reported angiosperm chloroplast genome. However, in Jatropha, the infA and the rps16 genes are non-functional. The inverted repeat (IR) boundary is within the rpl2 gene, and the 13 nucleotides at the ends of the two duplicate genes are different. Repeat analysis suggests the presence of 72 repeat regions (>30 bp) apart from the IR; of these, 48 were direct and 24 were palindromic repeats. Phylogenetic analysis of 81 protein coding chloroplast genes from 65 taxa by maximum parsimony, maximum likelihood and minimum evolution analyses at 100 bootstraps provide strong support for the placement of inaperturate crotonoids of which Jatropha is a member as sister to articulated crotonoids of which Manihot is a member.

Keywords

Jatropha curcas Chloroplast Genome Phylogeny Pyrosequencing Euphorbiaceae Angiosperms 

Supplementary material

11295_2010_303_MOESM1_ESM.doc (68 kb)
Supplementary Table 1(DOC 68 kb)

References

  1. 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
  2. Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ‘ridge pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21CrossRefPubMedGoogle Scholar
  3. Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112:1503–1518CrossRefPubMedGoogle Scholar
  4. Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, Jansen RK (2008) The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. Theor Appl Genet 116:723–737CrossRefPubMedGoogle Scholar
  5. Dixit R, Trivedi PK, Nath P, Sane PV (1999) Organization and post-transcriptional processing of the psb B operon from chloroplasts of Populus deltoides. Curr Genet 36:165–172CrossRefPubMedGoogle Scholar
  6. Higgins DG, Thompson JD, Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266:383–402CrossRefPubMedGoogle Scholar
  7. Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6:32CrossRefPubMedGoogle Scholar
  8. Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A 104:19369–19374CrossRefPubMedGoogle Scholar
  9. Jones N, Miller JH (1991) Jatropha curcas a multipurpose species for problematic sites. Land Resources Series 1Google Scholar
  10. Kim KJ, Lee HL (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11:247–261CrossRefPubMedGoogle Scholar
  11. King AJ, He W, Cuevas JA, Freudenberger M, Ramiaramanana D, Graham IA (2009) Potential of Jatropha curcas as a source of renewable oil and animal feed. J Exp Bot 60:2897–2905CrossRefPubMedGoogle Scholar
  12. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642CrossRefPubMedGoogle Scholar
  13. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12CrossRefPubMedGoogle Scholar
  14. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274CrossRefPubMedGoogle Scholar
  15. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13:645–658CrossRefPubMedGoogle Scholar
  16. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426PubMedGoogle Scholar
  17. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York, p 128Google Scholar
  18. Openshaw K (2000) A review of Jatropha curcas: an oil plant of unfulfilled promise. Biomass Bioenergy 19:1–15CrossRefGoogle Scholar
  19. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  20. Raubeson LA, Jansen RK (2005) In diversity and evolution of plants-genotypic and phenotypic variation in higher plants. In: Wallingford HH (ed) Chloroplast genomes of plants. CABI, Wallingford, pp 45–68Google Scholar
  21. Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174CrossRefPubMedGoogle Scholar
  22. Ravi V, Khurana JP, Tyagi AK, Khurana P (2006) The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes 3:49–59CrossRefGoogle Scholar
  23. Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (2006) Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7:222CrossRefPubMedGoogle Scholar
  24. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  25. Shimada H, Sugiura M (1991) Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19:983–995CrossRefPubMedGoogle Scholar
  26. Sudheer Pamidiamarri DV, Pandya N, Reddy MP, Radhakrishnan T (2009) Comparative study of interspecific genetic divergence and phylogenic analysis of genus Jatropha by RAPD and AFLP: genetic divergence and phylogenic analysis of genus Jatropha. Mol Biol Rep 36:901–907CrossRefPubMedGoogle Scholar
  27. Sujatha M, Reddy TP, Mahasi MJ (2008) Role of biotechnological interventions in the improvement of castor (Ricinus communis L.) and Jatropha curcas L. Biotechnol Adv 26:424–435CrossRefPubMedGoogle Scholar
  28. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  29. Tanaka M, Obokata J, Chunwongse J, Shinozaki K, Sugiura M (1987) Rapid splicing and stepwise processing of a transcript from the psbB operon in tobacco chloroplasts: determination of the intron sites in petB and petD. Mol Gen Genet 209:427–431CrossRefPubMedGoogle Scholar
  30. Tokuoka T (2007) Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed character evolution. J Plant Res 120:511–522CrossRefPubMedGoogle Scholar
  31. Tsudzuki T, Wakasugi T, Sugiura M (2001) Comparative analysis of RNA editing sites in higher plant chloroplasts. J Mol Evol 53:327–332CrossRefPubMedGoogle Scholar
  32. Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura S, Tsutsumi N, Kadowaki K (2008) Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol Biol Evol 25:1566–1575CrossRefPubMedGoogle Scholar
  33. Wurdack KJ, Hoffmann P, Chase MW (2005) Molecular phylogenetic analysis of uniovulate Euphorbiaceae (Euphorbiaceae sensu stricto) using plastid RBCL and TRNL-F DNA sequences. Am J Bot 92:1397–1420CrossRefGoogle Scholar
  34. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255CrossRefPubMedGoogle Scholar
  35. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. The University of Texas, AustinGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Mehar H. Asif
    • 1
  • Shrikant S. Mantri
    • 1
  • Ayush Sharma
    • 1
  • Anukool Srivastava
    • 1
  • Ila Trivedi
    • 1
  • Priya Gupta
    • 1
  • Chandra S. Mohanty
    • 1
  • Samir V. Sawant
    • 1
  • Rakesh Tuli
    • 1
  1. 1.Plant Molecular Biology and Genetic Engineering DivisionNational Botanical Research Institute Council of Scientific and Industrial ResearchLucknowIndia

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