Abstract
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity of plant specialized metabolism. So far, several terpenoid and alkaloid biosynthetic genes have been characterized with gene clusters in some plants. On the other hand, some modification genes involved in flavonoid and glucosinolate biosynthesis were found to arise via gene neo-functionalization. Although the occurrence of both types of metabolic evolution are different, the neighboring genes are generally regulated by the same or related regulation factors. Therefore, the translation-based approaches associated with genomics, and transcriptomics are able to be employed for functional genomics focusing on plant secondary metabolism. Here, we present a survey of the current understanding of neighboring genes involved in plant secondary metabolism. Additionally, a genomic overview of neighboring genes of four model plants and transcriptional co-expression network neighboring genes to detect metabolic gene clusters in Arabidopsis is provided. Finally, the insights functional genomics have provided concerning the evolution and mechanistic regulation of both the formation and operation of metabolic neighboring clusters is discussed.
Highlights
Plants produce a huge variety of specialized metabolites, which have been characterized as the defense metabolism of plants and the arsenals they develop come about via adaptation to and natural selection caused by ecological niches and environmental factors [1,2,3].Generally, the chemical diversity of plant specialized metabolites has been greatly expanded, either by horizontal gene transfer from other species, or by functional diversification following tandem gene duplication during metabolic evolution [4,5,6]
To discuss the detection of neighboring genes located in the gene cluster and neo-functionalization in model plants, we evaluated the duplication rate of metabolic genes in the genomes of A. thaliana, Oryza sativa, Solanum lycopersicum and Lotus japonica
Neighboring genes involved in plant specialized metabolism, such as metabolic gene cluster
Summary
Plants produce a huge variety of specialized metabolites (secondary metabolites), which have been characterized as the defense metabolism of plants and the arsenals they develop come about via adaptation to and natural selection caused by ecological niches and environmental factors [1,2,3]. It is important to note that gene duplication is considerably more prominent in plant genomes [24], and that this is a likely cause of the fact that they are metabolically considerably more diverse than other organisms [25,26] The fact that such metabolic polymorphism is generally found among natural accessions, but not among related plant species, except occasionally in the case of close relatives such as Arabidopsis lyrata, these neo-functionalized genes are generally regarded to be recently evolved genes. Since on average, 65% of annotated genes in plant genomes have a duplicate copy [27], the detection of key genomic region and genes of species specific specialized metabolism is highly complex This has been addressed computationally with the programs PhytoClust [28] and PlantiSmash [29] being highly usable tools that allowed web-based searches for gene clusters. We present a case study of the approach of detecting metabolic gene clusters, via co-expression analyses focused on plant specialized metabolism
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