Meliaceae genomes provide insights into wood development and limonoids biosynthesis

Abstract

Summary Meliaceae is a useful plant family owing to its high‐quality timber and its many limonoids that have pharmacological and biological activities. Although some genomes of Meliaceae species have been reported, many questions regarding their unique family features, namely wood quality and natural products, have not been answered. In this study, we provide the whole‐genome sequence of Melia azedarach comprising 237.16 Mb with a contig N50 of 8.07 Mb, and an improved genome sequence of Azadirachta indica comprising 223.66 Mb with a contig N50 of 8.91 Mb. Moreover, genome skimming data, transcriptomes and other published genomes were comprehensively analysed to determine the genes and proteins that produce superior wood and valuable limonoids. Phylogenetic analysis of chloroplast genomes, single‐copy gene families and single‐nucleotide polymorphisms revealed that Meliaceae should be classified into two subfamilies: Cedreloideae and Melioideae. Although the Meliaceae species did not undergo additional whole‐genome duplication events, the secondary wall biosynthetic genes of the woody Cedreloideae species, Toona sinensis, expanded significantly compared to those of A. indica and M. azedarach, especially in downstream transcription factors and cellulose/hemicellulose biosynthesis‐related genes. Moreover, expanded special oxidosqualene cyclase catalogues can help diversify Sapindales skeletons, and the clustered genes that regulate terpene chain elongation, cyclization and modification would support their roles in limonoid biosynthesis. The expanded clans of terpene synthase, O‐methyltransferase and cytochrome P450, which are mainly derived from tandem duplication, are responsible for the different limonoid classes among the species. These results are beneficial for further investigations of wood development and limonoid biosynthesis.

Wood of trees: Cellular structure, molecular formation, and genetic engineering

“…The genome sequences of Melia azedarach , Azadirachta indica and Toona sinensis (also called Chinese mahogany) from the Meliaceae family have been compared. The results show the genes related to cellulose and hemicellulose biosynthesis, as well as their corresponding regulatory transcription factors, are significantly expanded in Toona sinensis (Cui et al, 2023). Ochroma pyramidale , also known as balsa, is a fast‐growing tree the wood of which is soft and light, while Mesua ferrea , often called ironwood, generates wood with a high density and hardness.…”

A comprehensive review of azadirachtin: physicochemical properties, bioactivities, production, and biosynthesis

“…Year 2012 [8] 2015 [112] 2016 [9] 2022 [16] 2022 [15] 2022 [15] Tissue Root, leaf, pathway from 2,3-epoxidized squalene to azadirachtin A. It was suggested that 2,3-epoxidized squalene initially forms a Euphorbia dienol intermediate under enzymatic catalysis, followed by a series of reactions leading to the production of azadirachtin A.…”

“…However, this inference was deemed inconclusive at the time [115] . Subsequently, the abundant azadirachtin genome and transcriptome information available to the public was analyzed, including the complementary DNA (cDNA) library [7] , draft genome [8][9] , EST libraries [10][11] , transcriptome data [8,[12][13][14] , and chromosome-level genome data [15][16] . This search encompassed genes from the MVA pathway, MEP pathway, 2,3-oxosqualene synthesis, and cytochrome P450 (CYP450s).…”

“…Comparative genomic analysis revealed that most neem-specific TPS and CYP genes reside in a terpene-associated cluster on chromosome 13, suggesting their crucial role in terpene biosynthesis in neem. Subsequently, Cui et al [15] assembled a chromosome-level whole-genome sequence spanning 237.16 Mb. Contig N50 improved nearly 400-fold compared with that of the reference genome, offering high base accuracy and continuity.…”

“…Recently, significant breakthroughs have been made in azadirachtin biosynthesis. Many studies have examined the azadirachtin genome and completed transcriptome analyses, including complementary DNA (cDNA) library [7] , draft genome [8][9] , expressed sequence tag (EST) libraries [10][11] , transcriptome data [8,[12][13][14] , and chromosome-level genome [15][16] . Through systematic transcriptome and genome exploration, coupled with co-expression, phylogenetic, and comparative analysis, Osbourn et al achieved a transformative breakthrough by successfully converting the intermediate skeletal compound from 2,3-oxidized squalene to tirucalla-7,24-dien-3β-ol [17] .…”