Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree.
Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Nagesh A
NA
Kuravadi
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Vijay
V
Yenagi
Metabolomics Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Kannan
K
Rangiah
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.|Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, India.
H B
HB
Mahesh
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Anantharamanan
A
Rajamani
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Meghana D
MD
Shirke
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Heikham
H
Russiachand
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Ramya Malarini
RM
Loganathan
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Chandana
C
Shankara Lingu
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Shilpa
S
Siddappa
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Aishwarya
A
Ramamurthy
Plant Tissue Culture Laboratory, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, India.
B N
BN
Sathyanarayana
Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India.
Malali
M
Gowda
A. indica; Annotation; Azadirachtin; Next generation sequencing