Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories ( Ipomoea )

Abstract

Abstract. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (x = d N /d S ) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.

Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes

“…Most species containing more than two DFR gene copies also possess multiple copies of other ABP genes. For example, there are two copies of CHS in Zea 66, at least five copies of CHS in Ipomoea 67, at least eight copies of CHS and one to two copies of CHI in Medicago 68, at least 13 copies of CHS , four copies of PKR , etc. in Lotus 69, at least six CHS and seven CHS- like genes, two F3′5′H copies, etc.…”

Elevated Gene Expression inChalcone SynthaseEnzyme Suggests an Increased Production of Flavonoids in Skin and Synchronized Red Cell Cultures of North American Native Grape Berries

“…This leads to the diversity of phenolic compounds such as lignins and phytoalexins (Winkel-Shirley, 2001;Szalma et al, 2002). Genes encoding CHS constitute a multigene family in which the copy number varies among the plant species, and functional divergence appears to have repeatedly occurred (Tuteja et al, 2004;Yang et al, 2004). The expression of the CHS gene in fruit tissue is developmentally regulated and associated with fruit coloring (Aharoni and O'Connell, 2002;Kumar and Ellis, 2003).…”

Bioinformatics in China: A Personal Perspective

“…Their findings settled previous disputes over whether rice was an ancient aneuploid or an ancient polyploidy, bringing the two contradictory sides to agreement in the form of a graciously coauthored Commentary [85]. In addition to whole genomes, the evolution of many important plant gene families was also studied in detail, such as transcription factor families [86] and enzymes [87]. A group studied the origination of new genes in rice and found a surprisingly high number of retrogenes as well as chimeric genes originated by retroposition, suggesting that retroposition is an important mechanism that governs gene evolution in rice and other grass species [88].…”