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Molecular phylogenetic analysis of key Jatropha species inferred from nrDNA ITS and chloroplast (trnL-F and rbcL) sequences

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Abstract

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.

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References

  • Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    Article  CAS  PubMed  Google Scholar 

  • Banerji R, Chowdhury A, Misra G, Sudarsanan G, Verma S, Srivastava G (1985) Jatropha seed oils for energy. Biomass 8:277–282

    Article  CAS  Google Scholar 

  • Basha S, Sujatha M (2009) Genetic analysis of Jatropha species and interspecific hybrids of Jatropha curcas using nuclear and organelle specific markers. Euphytica 168:197–214

    Article  CAS  Google Scholar 

  • Basha S, Francis G, Makkar H, Becker K, Sujatha M (2009) A comparative study of biochemical traits and molecular markers for assessment of genetic relationships between Jatropha curcas L. germplasm from different countries. Plant Sci 176:812–823

    Article  CAS  Google Scholar 

  • Dehgan B (1982) Comparative anatomy of the petiole and infrageneric relationships in Jatropha (Euphorbiaceae). Am J Bot 69:1283–1295

    Article  Google Scholar 

  • Dehgan B (1984) Phylogenetic significance of interspecific hybridization in Jatropha (Euphorbiaceae). Syst Bot 9:467–478

    Article  Google Scholar 

  • Dehgan B, Schutzman B (1994) Contributions toward a monograph of neotropical Jatropha: phenetic and phylogenetic analyses. Ann Mo Bot Gard 81:349–367

    Article  Google Scholar 

  • Dehgan B, Webster GL (1979) Morphology and infrageneric relationships of the genus Jatropha (Euphorbiaceae), vol 74. University of California Press, California

    Google Scholar 

  • Dhillon R, Hooda M, Jattan M, Chawla V, Bhardwaj M, Goyal S (2009) Development and molecular characterization of interspecific hybrids of Jatropha curcas× J. integerrima. Indian J Biotechnol 8:384–390

    CAS  Google Scholar 

  • Edrisi SA, Dubey RK, Tripathi V, Bakshi M, Srivastava P, Jamil S, Singh H, Singh N, Abhilash P (2015) Jatropha curcas L.: a crucified plant waiting for resurgence. Renew Sustain Energy Rev 41:855–862

    Article  Google Scholar 

  • Farris JS, Källersjö M, Kluge AG, Bult C (1994) Testing significance of incongruence. Cladistics 10:315–319

    Article  Google Scholar 

  • Fay MF, Swensen SM, Chase MW (1997) Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). Kew Bull 52:111–120

    Article  Google Scholar 

  • Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709

    CAS  PubMed  PubMed Central  Google Scholar 

  • Heller J (1996) Physic nut. Jatropha curcas L. Promoting the conservation and use of underutilized and neglected crops.1. PhD Thesis, Institute of Plant Genetic and Crop Plant Research, Gatersleben, and International Plant Genetic Resource Institute, Rome

  • Hemming C, Radcliffe-Smith A (1987) A revision of the Somali species of Jatropha (Euphorbiaceae). Kew Bull 42:103–122

    Article  Google Scholar 

  • 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 60:2897–2905

    Article  CAS  PubMed  Google Scholar 

  • Kumar RS, Parthiban K, Rao MG (2009) Molecular characterization of Jatropha genetic resources through inter-simple sequence repeat (ISSR) markers. Mol Biol Rep 36:1951–1956

    Article  Google Scholar 

  • Mason-Gamer RJ, Orme NL, Anderson CM (2002) Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets. Genome 45:991–1002

    Article  CAS  PubMed  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci 76:5269–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nylander J (2004) MrModeltest v2.2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala

  • Olowokudejo J (1993) Comparative epidermal morphology of West African species of Jatropha L. (Euphorbiaceae). Bot J Linn Soc 111:139–154

    Article  Google Scholar 

  • Pamidimarri DS, Reddy MP (2014) Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis. Mol Biol Rep 41:3225–3234

    Article  Google Scholar 

  • Pamidimarri DS, Chattopadhyay B, Reddy MP (2009) Genetic divergence and phylogenetic analysis of genus Jatropha based on nuclear ribosomal DNA ITS sequence. Mol Biol Rep 36:1929–1935

    Article  Google Scholar 

  • Parthiban K, Kumar RS, Thiyagarajan P, Subbulakshmi V, Vennila S, Rao MG (2009) Hybrid progenies in Jatropha-a new development. Curr Sci 96:815–823

    CAS  Google Scholar 

  • Ram SG, Parthiban K, Kumar RS, Thiruvengadam V, Paramathma M (2008) Genetic diversity among Jatropha species as revealed by RAPD markers. Genet Resour Crop Evol 55:803–809

    Article  CAS  Google Scholar 

  • Reddy K, Swamy N, Bahadur B (1987) Cross-incompatibility between Ricinus and Jatropha. Plant Cell Incompat Newslett 19:60–65

    Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  CAS  PubMed  Google Scholar 

  • Sudheer PD, Mastan SG, Rahman H, Prakash CR, Singh S, Reddy MP (2011) Cross species amplification ability of novel microsatellites isolated from Jatropha curcas and genetic relationship with sister taxa. Mol Biol Rep 38:1383–1388

    Article  CAS  PubMed  Google Scholar 

  • Sujatha M (1996) Genetic and tissue culture studies in castor (Ricinus communis L.) and related genera. Ph.D. thesis, Osmania University, Hyderabad

  • Sujatha M (2006) Genetic improvement of Jatropha curcas L. possibilities and prospects. Indian J Agrofor 8:58–65

    Google Scholar 

  • Sujatha M, Prabakaran A (2003) New ornamental Jatropha hybrids through interspecific hybridization. Genet Resour Crop Evol 50:75–82

    Article  CAS  Google Scholar 

  • Sujatha M, Bahadur B, Reddy TP (2013) Interspecific hybridization in the genus Jatropha. In: Bahadur B, Sujatha M, Carels N (eds) Jatropha, challenges for a new energy crop, vol 2. Springer, New York, pp 423–443

    Chapter  Google Scholar 

  • Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony, Version 4.0b10. Sinauer Associates, Sunderland

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanya P, Taeprayoon P, Hadkam Y, Srinives P (2011) Genetic diversity among Jatropha and Jatropha-related species based on ISSR markers. Plant Mol Biol Report 29:252–264

    Article  Google Scholar 

  • Thompson JD, Gibson T, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics, Chapter 2: Unit 2.3

  • Tokuoka T, Tobe H (2006) Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str. J Plant Res 119:599–616

    Article  CAS  PubMed  Google Scholar 

  • Watterson G (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276

    Article  CAS  PubMed  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protoc 18:315–322

    Google Scholar 

  • Ye M, Li C, Francis G, Makkar HP (2009) Current situation and prospects of Jatropha curcas as a multipurpose tree in China. Agrofor Syst 76:487–497

    Article  Google Scholar 

  • Zhang Z, Liu B, Tang L, Chen F (2011) Genetic diversity and genetic relationship of Jatropha curcas between China and Southeast Asian revealed by amplified fragment length polymorphisms. Afr J Biotechnol 10:2825–2832

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The research was partially supported by grants from the National “12th Five-Year” Science and Technology Support project of China (No. 2011BAD22B08).We thankfully acknowledge the Tropical Eco-agriculture Institute, Yunnan Academy of Agricultural Sciences and South China Botanical Garden, Chinese Academy of Sciences for kindly providing the plant materials.

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Authors and Affiliations

  1. Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, Sichuan, People’s Republic of China

    Guo-ye Guo, Sheng-hua Wang, Ying Xu, Lin Tang & Fang Chen

  2. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People’s Republic of China

    Guo-ye Guo & Mao-qun Yu

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  1. Guo-ye Guo
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  2. Sheng-hua Wang
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  4. Lin Tang
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  5. Mao-qun Yu
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  6. Fang Chen
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Correspondence to Fang Chen.

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Guo, Gy., Wang, Sh., Xu, Y. et al. Molecular phylogenetic analysis of key Jatropha species inferred from nrDNA ITS and chloroplast (trnL-F and rbcL) sequences. Genes Genom 38, 557–566 (2016). https://doi.org/10.1007/s13258-016-0406-6

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  • DOI: https://doi.org/10.1007/s13258-016-0406-6

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