Skip to main content

Molecular systematics of Indian Crotalaria (Fabaceae) based on analyses of nuclear ribosomal ITS DNA sequences


Crotalaria L. (Fabaceae) comprises approximately 700 species that are distributed in tropical and subtropical regions of the world. In India, it is the largest legume genus with 92 species. Sequences of the nuclear internal transcribed spacer from species representing all the six recognized sections of Indian Crotalaria were subjected to phylogenetic analyses. Ancestral state reconstructions were done for two morphological characters, corolla keel beak, and leaf form. Analyses reveal five major well-supported clades within a monophyletic Crotalaria. Clade 1 has members with rostrate-spirally twisted keel beaks while the remaining four clades comprise members with keel beaks rostrate-not spirally twisted. Clade 1 further bifurcates into two clades characterized by differences in leaf morphology: (1a) contains species with simple leaves belonging to section Calycinae, section Crotalaria subsection Crotalaria and subsection Bractetae and multifoliolate leaves belonging to section Crotalaria subsection Polyphyllae (1b) contains species with trifoliate leaves belonging to section Dispermae, section Crotalaria subsection Longirostres. Sub-clade iii in Clade 1a contains four species complexes, each forming a monophyletic group. Of these one comprising C. madurensis, C. subperfoliata, C. shevaroyensis, and C. longipes is endemic to a region in southern India. Each of the others contains one endemic species and one widespread species that is sympatric with the endemic one (C. hirta and C.mysorensis; C. epunctata and C. albida; C. clarkei and C. triquetra). The present study suggests that: (1) all members of section Calycinae and most members of section Crotalaria form a clade, (2) members of section Crotalaria subsection Longirostres and section Dispermae form a distinct clade, (3) twisting of the keel beak is an apomorphy within the genus, (4) there is a reversal to keel beak rostrate-not spirally twisted in C. shevaroyensis and an independent origin of a rostrate-spirally twisted keel beak in C. humilis, and (5) the trifoliolate condition is a plesiomorphy in the genus and the simple leaf condition an apomorphy; there is a single reversal to the trifoliolate condition in C. orixensis. The current morphological classification system of Indian Crotalaria species includes six sections, but these circumscriptions are not supported by the molecular data.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3


  • Ansari AA (2008) Crotalaria L. in India. Bishen Singh Mahendra Pal Singh, Dehra Dun

  • Arroyo MTK (1981) Breeding systems and pollination biology in Leguminosae. In: Polhill RM, Raven PH (eds) Advances in Legume Systematics, vol 2. Royal Botanic Gardens, Kew, pp 723–769

    Google Scholar 

  • Baker JG (1876) Order L. Leguminosae. In: Hooker JD (ed) The Flora of British India, vol. II. Sabiaceae to Cornaceae. Reeve and Co Ltd., London

  • Bisby FA, Polhill RM (1973) The role of taximetrics in angiosperm taxonomy II. Parallel taximetric and orthodox studies in Crotalaria L. New Phytol 72:727–742

    Article  Google Scholar 

  • Boatwright JS, le Roux MM, Wink M, Morozova T, van Wyk BE (2008) Phylogenetic relationships of tribe Crotalarieae (Fabaceae) inferred from DNA sequences and morphology. System Bot 33:752–761

    Article  Google Scholar 

  • DNA Baser Sequence Assembler v3.x (2011) Heracle Biosoft SRL.

  • Etcheverry AV, Protomastro JJ, Westerkamp C (2003) Delayed autonomous self-pollination in the colonizer Crotalaria micans (Fabaceae : Papilionaceae): structural and functional aspects. Plant Sys Evol 239:15–28

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution Minimal change for a specific tree topology. System Zool 20:406–416

    Article  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum Likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754–755

    Article  PubMed  CAS  Google Scholar 

  • Le Roux MM, Van Wyk BE (2012) The systematic value of flower structure in Crotalaria and related genera of the tribe Crotalarieae (Fabaceae). Flora (in press)

  • Lewis G, Schrire B, Mackinder B, Lock M (eds) (2005) Legumes of the world. Royal Botanical Gardens, Kew

    Google Scholar 

  • Li J, Sun H, Polhill RM, Gilbert MG (2010) Crotalaria in Flora of China. In: Zhengyi W, Raven PH, Deyuan H (eds) Fabaceae, vol 10. Science press and Missouri Botanical Garden, Beijing, p 105

  • Maddison WP, Maddison DR (2009) Mesquite: A modular system for evolutionary analyses. Version 2.72.

  • Mangotra R, Bhargava R (1987) Carbohydrate Patterns as Aids in the Taxonomy of Genus Crotalaria. Proc Natl Acad Sci India Sect B (Biol Sci) 57:423–429

    CAS  Google Scholar 

  • Nayar MP, Sastry ARK (1987) Red data book of Indian plants Vol 1. Botanical survey of India, Calcutta

    Google Scholar 

  • Polhill RM (1968) Micellaneous notes on African species of Crotalaria L. II. Kew Bull 22:169–348

    Article  Google Scholar 

  • Polhill RM (1982) Crotalaria in Africa and Madagascar. Royal Botanical Gardens, Kew

    Google Scholar 

  • Posada D (2008) jModel test. phylogenetic model averaging. Mol Biol Evol 25:1253–1256

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbour- joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sibichen MT, Nampy S (2007) Crotalaria kurisumalayana Sibichen & Nampy (Fabaceae), a new species from India. Candollea 62(1):105–108

    Google Scholar 

  • Swofford DL (1996) PAUP*: Phylogenetic analyses using parsimony (*and other methods), version 4.0. Sinauer, Sunderland, Massachessets

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analyses using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analyses tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • White TM, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA for phylogenetics. Academic Press, San Diego, pp 315–321

    Google Scholar 

Download references


Shweta Subramaniam is thankful to University Grants Commission for providing a Junior Research Fellowship for carrying out this research. Grant support from the University of Delhi to Arun K. Pandey is thankfully acknowledged. We thank Dr. B. Subramaniam, retired Scientist G, Council of Scientific and Industrial Research, India for accompanying the senior author during plant collection trips. We also thank Dr. Ravikumar, Mr. Jey Parakash, Foundation for Revitalization of Local Health Traditions, Bengaluru, Dr. Santosh Nampy and group, Kerala, Dr. Yadav and group, Kolhapur, Dr. Janarthanam and group, Goa, India for their help in field collections. We also gratefully acknowledge the valuable suggestions of anonymous reviewers whose comments greatly improved this manuscript.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Arun K. Pandey.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Subramaniam, S., Pandey, A.K., Geeta, R. et al. Molecular systematics of Indian Crotalaria (Fabaceae) based on analyses of nuclear ribosomal ITS DNA sequences. Plant Syst Evol 299, 1089–1106 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Crotalaria
  • ITS
  • Phylogeny
  • Character reconstruction