Plants have diverse secondary metabolites also known as natural products (Dixon and Strack 2003). Plants natural products are formed by an enzyme-mediated chemical reaction and together form biosynthetic pathways. Genes for specific biosynthetic pathways are localized in plant genomes in biosynthetic gene clusters (BGCs) (Polturak and Osbourn 2021). Phenomenon of gene clustering is not rare, over 30 BGC are reported from lower to higher plants. They encompass different class of compounds including terpenoids, alkaloids, fatty acids, polyketides and cyanogenic glycosides which exhibit activity against various types of pest and pathogens as well as against competing plants (Polturak and Osbourn 2021). These class of compounds also include phytoanticipins and phytoalexins compounds in plants that confer resistance against the pathogens as well confer resistance to abiotic stress such as component of leaf waxes, which protect plants from desiccation (Polturak and Osbourn 2021). Six pathogen induced biosynthetic pathways share a common regulatory network and form part of an orchestrated defense response. The wheat genome reveals that each of these pathways are encoded by BGCs (Poltruk et al., 2022). These BGCs produce flavonoid and terpenes which may act as phytoalexins or defense-related signaling molecules (Polturak et al., 2022).
Plant metabolic genes are organized in many different patterns in genomes. The arrangement can be from a single randomly located gene to a complete clustered pathway: the passage from disorder to order. The key categories to describe gene organization are tandem arrays, gene pairs and BGCs, variations to these phenomena are common, including gene pairs and split BGCs (Smit and Lichman 2022). Variation within metabolically important genomic region such as within BGC, can be seen at both inter- as well as at intra-species level. The differences observed include presence-absence variations (PAV), copy number variation (CNV) and larger genomic changes such as haplotype differences and chromosomal rearrangements. (Smit and Lichman 2022).
The biosynthetic genes of some specialized plant metabolites seem to be clustered in the genome of higher plants. BGCs involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and phytoalexins momilactones A are found in barnyard grass (Echinochloa crus-galli) genome, as well as in maize and rice (Guo et al., 2017). Momilactones are defense compounds produced in rice and barnyard grass by family-conserved BGCs (Mao et al., 2020). The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, whereas the phytoalexin momilactone A gene cluster is activated in response to infection caused by pathogen Pyricularia oryzae (Guo et al., 2017). The gene clusters for biosynthesis of diterpene compound momilactone A have evolved both in rice and independently in bryophyte Calohypnum plumiformae (Shimura et al., 2007, Mao et al., 2020). Arabidopsis thaliana contains four BGCs producing triterpenes (Cawood and Ton 2025). A. thaliana produces range of specialized triterpene thalianin, thalianyl fatty acid esters and arabidin derived from BGCs that shapes the A. thaliana specific root microbial community (Huang et al., 2019). Several of these clustered Arabidopsis genes may be involved in defense against root pathogens (Huang et al., 2019). Plants shape their rhizosphere microbiome and enhance microbial activity to suppress pathogens in the rhizosphere (Berendsen et al., 2012). Oat produces antimicrobial avenacins a triterpenoid saponin in the root providing protection against pathogens is a product of clustered gene in oat genome (Qi et al., 2004; Mao et al., 2020). Mendes et al.(2023) after analysis obtained five candidate BGCs with terpenes as the representative BGC class in both rhizosphere and endosphere. The biosynthesis of terpenes by plants and bacteria suppress Fusarium oxysporum infection(Li et al., 2018; Reddy et al., 2020).
Diterpenoid phytoalexin is chemical defense against pathogens and enhance disease resistance in rice. The BGCs and few non-BGC genes are involved for rice phytoalexin biosynthesis (Wang et al., 2023). Cultivated rice (Oryza sativa) produces antimicrobial diterpene phytoalexin phytocassanes and momilactones and many of their biosynthetic gene are clustered on chromosome 2 and 4 respectively (Miyamoto et al., 2016). The closely related wild relatives to Oryza sativa within the same AA genome lineage share both the chromosome 4 momilactone and chromosome 2 phytocassane BGCs, the more distant Oryza lineage show variation. Momilactone BGC is absent in Oryza brachyantha and Leersia perrieri but present in Oryza punctata. In contrast phytocassane BGC is present in L. perrieri but absent inO. brachyantha and O. punctata, where it is replaced by CYPs (cytochrome P450s) (Smit and Lichman 2022). The pathogen induced BGC in bread wheat produces an O-methylated isoflavone,5-hydroxy-2’,4’,7-trimethoxyisoflavone known as triticein (Polturak et al., 2023). In vitro antimicrobial activity of triticein is suggested to have a defense related role (Polturak et al., 2023).
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BIOLOGICAL PROCESSES- A NATURE'S GIFT 