Abstract
BackgroundThe available data demonstrate that even in universal metabolic pathways, some species-specific regulatory features of structural genes are present. For instance, in the anthocyanin biosynthesis pathway (ABP), genes may be regulated by ABP-specific regulatory factors, and their expression levels may be strongly associated with anthocyanin pigmentation, or they may be expressed independently of pigmentation. A dataset of orthologous ABP genes (Chs, Chi, F3h, F3’h, Dfr, Ans) from monocot and dicot plant species that have distinct gene regulation patterns and different types of pollination was constructed to test whether these factors affect the evolution of the genes.ResultsUsing a maximum likelihood approach, we demonstrated that although the whole set of the ABP genes is under purifying selection, with greater selection acting on the upstream genes than on the downstream genes, genes from distinct groups of plant species experienced different strengths of selective pressure. The selective pressure on the genes was higher in dicots than in monocots (F3h and further downstream genes) and in pollinator-dependent plants than in pollinator-independent species (Chi and further downstream genes), suggesting an important role of pollination type in the evolution of the anthocyanin biosynthesis gene network. Contrasting effects of the regulation patterns on evolution were detected for the F3h and Dfr genes, with greater selective pressure on the F3h gene in plant species where the gene expression was not strongly associated with pigmentation and greater selective pressure on Dfr in plant species where the gene expression was associated with pigmentation.ConclusionsWe demonstrated the effects of pollination type and patterns of regulation on the evolution of the ABP genes, but the evolution of some of the genes could not be explained in the framework of these factors, such as the weaker selective pressure acting on Chs in species that attract pollinators or the stronger selective pressure on F3h in plant species where the gene expression was not associated with pigmentation. The observations suggest that additional factors could affect the evolution of these genes. One such factor could be an effect of gene duplication with further division of functions among gene copies and relaxed selective pressure acting on them. Additional tests with an appropriate dataset combining data on duplicated gene sequences and their functions in the flavonoid biosynthesis pathway are required to test this hypothesis.
Highlights
The available data demonstrate that even in universal metabolic pathways, some species-specific regulatory features of structural genes are present
The dataset was constructed based on Identification of the orthologous set of anthocyanin biosynthesis genes and their regulatory patterns Sequences of the six anthocyanin biosynthesis pathway (ABP) genes (Chs, Chi, F3h, F3’h, Dfr, Ans) in monocots (Aegilops tauschii Coss., Anthurium andraeanum Linden ex André, Hordeum vulgare L., Oryza sativa L., Triticum aestivum L., Triticum urartu Thum. ex Gandil., Zea mays L.) and dicots (Arabidopsis lyrata (L.) O’Kane & Al-Shehbaz, Arabidopsis thaliana (L.) Heynh., Malus domestica Borkh., Solanum tuberosum L., Vitis amurensis Rupr., Vitis vinifera L.), with the most characterized pathways of structural genes, and their regulatory patterns were retrieved from databases (Additional file 2: Table S1)
The groups of monocots and dicots were distinguished in the tree, and the tree corresponded to the taxonomic classifications of the plant species chosen for the analysis
Summary
The available data demonstrate that even in universal metabolic pathways, some species-specific regulatory features of structural genes are present. The anthocyanin biosynthesis pathway (ABP) produces the pigments responsible for the coloration of different parts of a plant It shares a number of common enzymes with pathways that produce diverse classes of flavonoids (Additional file 1: Figure S1), which serve important physiological functions, including protection from pathogens and unfavorable environmental factors, signaling and interactions with symbionts, promotion of pollen tube growth, and mediation of hormone transport [1,2,3]. The structural genes of the ABP are common to all angiosperms and have been characterized in many plant species They can be divided into two groups: upstream genes, encoding chalcone synthase (CHS), chalconeflavanone isomerase (CHI), flavanone 3-hydroxylase (F3H), and dihydroflavonol 4-reductase (DFR), synthesize precursors for one or more non-anthocyanin flavonoid pathways, and downstream genes, encoding anthocyanidin synthase (ANS), glycosyltransferase (GT), rhamnosyltransferase (RT), acetyltransferase (AT), and methyltransferase (MT), are specific to the anthocyanin pathway (Additional file 1: Figure S1). No relationships between the position of the genes in a pathway and selective constraints have been found when studying the phenylpropanoid pathway in Arabidopsis thaliana [11], the gibberellin pathway in the Oryzeae tribe [12], or the starch pathway in Oryza sativa [13]
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