title: A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore 560100, India.
authors.forename: Neeraja M
authors.initials: NM
authors.lastname: Krishnan
authors.forename: Swetansu
authors.initials: S
authors.lastname: Pattnaik
authors.forename: Prachi
authors.initials: P
authors.lastname: Jain
authors.forename: Prakhar
authors.initials: P
authors.lastname: Gaur
authors.forename: Rakshit
authors.initials: R
authors.lastname: Choudhary
authors.forename: Srividya
authors.initials: S
authors.lastname: Vaidyanathan
authors.forename: Sa
authors.initials: S
authors.lastname: Deepak
authors.forename: Arun K
authors.initials: AK
authors.lastname: Hariharan
authors.forename: Pg Bharath
authors.initials: PB
authors.lastname: Krishna
authors.forename: Jayalakshmi
authors.initials: J
authors.lastname: Nair
authors.forename: Linu
authors.initials: L
authors.lastname: Varghese
authors.forename: Naveen K
authors.initials: NK
authors.lastname: Valivarthi
authors.forename: Kunal
authors.initials: K
authors.lastname: Dhas
authors.forename: Krishna
authors.initials: K
authors.lastname: Ramaswamy
authors.forename: Binay
authors.initials: B
authors.lastname: Panda
mesh_terms: D031601:Azadirachta / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D001482:Base Composition; D018745:Genome, Plant; D005810:Multigene Family; D010575:Pesticides / Q000378:metabolism; D010802:Phylogeny; D010946:Plants, Medicinal / Q000737:chemistry / Q000145:classification / Q000235:genetics; D017422:Sequence Analysis, DNA; D013729:Terpenes / Q000737:chemistry / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010575:Pesticides; D013729:Terpenes