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A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Neeraja M Krishnan1, Swetansu Pattnaik12, Prachi Jain1, Prakhar Gaur1, Rakshit Choudhary1, Srividya Vaidyanathan1, Sa Deepak1, Arun K Hariharan1, PG Bharath Krishna1, Jayalakshmi Nair1, Linu Varghese1, Naveen K Valivarthi1, Kunal Dhas1, Krishna Ramaswamy1 and Binay Panda12*

Author affiliations

1 Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore, 560100, India

2 Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India

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Citation and License

BMC Genomics 2012, 13:464  doi:10.1186/1471-2164-13-464

Published: 9 September 2012



The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach.


The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs.


This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.

A. Indica; Neem; Meliaceae; Genome; Transcriptome; Repeats; Phylogeny; Terpenoid biosynthesis; Pesticide and transcript expression