Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

Abstract

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.

Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

“…Alignment to the Azadirachta indica A. Juss. chloroplast genome [35] revealed that the largest contig included two inverted repeat regions separated by the large single-copy region. The two remaining 19 Kbp contigs represented both orientations of the small single-copy region; we retained the small single-copy contig that matched the orientation of the A. indica chloroplast genome.…”

“…5; see Additional file 1: Figure S3). This phylogeny included the CEOD-NYBG reference, chloroplast genomes we prepared by reference-guided assembly, and two publicly available chloroplast genomes from the Meliaceae: A. indica NC_023792.1 and C. odorata NC_037251.1 [35, 40]. Our alignment for all taxa contained 11,950 SNPs, 1695 of which were segregating within Cedrela taxa (~ 7.6 SNPs/Kbp).…”

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

“…Within breeding programs, various types of molecular markers, such as random amplified polymorphic DNA (RAPD), ribosomal DNA (rDNA), inter-simple sequence repeat (ISSR), sequence characterised amplified region (SCAR), and simple sequence repeat (SSR), have been utilized [ 2 , 3 , 4 , 5 , 6 , 7 ]. Notably, SSRs and single nucleotide polymorphism (SNP) markers are propounded in genetic and plant breeding applications [ 8 ].…”

Induction of Autophagy and Apoptosis via PI3K/AKT/TOR Pathways by Azadirachtin A in Spodoptera litura Cells

“…Azadirachtin A (AZA) is an effective botanical insecticide that is primarily isolated from the seed kernel of the neem tree Azadirachta indica A. Juss (Meliaceae) 18 19 20 and has been widely used as an alternative to synthetic pesticides for controlling various types of agricultural pests because of its non-persistence in the environment and low toxicity against non-target beneficial organisms 21 22 23 . AZA has potent antifeedant and growth inhibitory activities against insects.…”