Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

PeerJ

Meghana D. Shirke¹  HB Mahesh¹  Chandana Shankara Lingu¹  Shilpa Siddappa¹  Aishwarya Ramamurthy¹  Malali Gowda¹  Vijay Yenagi¹  Nagesh A. Kuravadi¹  Heikham Russiachand¹  Ramya Malarini Loganathan¹  Anantharamanan Rajamani¹  Kannan Rangiah²  BN Sathyanarayana³ 

[1] Genomics Laboratory, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India;Metabolomics Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Bangalore, Karnataka, India;Plant Tissue Culture Laboratory, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, India;

关键词: Next generation sequencing;    Annotation;    A. indica;    Azadirachtin;   

DOI  :  10.7717/peerj.1066

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown