The Evolutionary Rate Variation Among Genes of MVA and MEP Pathways in Plant Terpenoid Biosynthesis

Abstract

Background: Terpenoids are one of the most important compounds in plants, play an significant biological defense and developmental roles in numerous plant species, and widely used for industrial chemicals. Many previous studies have completed the identification of terpenoid biosynthetic pathway and related genes. However, few studies have focused on the molecular evolution analysis of terpenoid pathway genes in plants. In this study, we researched the evolutionary rate variation pattern of 16 terpenoid pathway genes in 12 species with a broad taxonomic span. Results: We retrieved 14 genes in MVA and MEP pathways and 2 extra genes from 12 species, respectively. The evolutionary parameters dN values and dN/ dS ratios are varied significantly among genes, and the dN/ dS ratios of most genes are varied substantially among lineages. The MVA and MEP pathways genes have different evolutionary rate variation pattern, although no significant difference in dN/ dS ratios between two pathways genes. For MVA pathway, the downstream genes exhibits the greater dN/ dS ratio than upstream genes. For MEP pathway, the three midstream genes evolves more rapidly than other genes, and most of MEP pathway genes were detected the signature of positive selection under random sites models. Moreover, the dN/ dS ratios of MVA and MEP pathways genes are negatively correlated with pathway position and PPI, and coding sequence length, respectively. Conclusions: Taken together, the results indicated that the evolutionary rate variation of MVA pathway genes is mainly attributed to differential selective constraint rather than the positive selection. However, the differential selective constraint relaxation and positive selection collectively shaped the evolutionary rate heterogeneity of MEP pathway genes.

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

“…Examining codon usage bias allows us to discern the distinct roles played by these forces in shaping the genetic architecture of the species [ 17 , 18 ]. Moreover, by scrutinizing the dN/dS substitution rates among paralogous genes within M. lotungensis , we can shed light on the evolutionary trajectory of gene families, gaining insights into the molecular mechanisms that underpin the species’ adaptations and vulnerabilities [ 19 , 20 , 21 ].…”