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

Abstract

Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.

Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression

“…8 ) and was lower in Shepody, the control. DFRa expression was greater than DFRb expression in RedR3 but less than that in PurpleR2, consistent with the differences in cyanidin and delphinidin content between these varieties [ 40 ]: at the higher DFRa-type transcript spliceosomes content, cyanidin 3-O-galactoside, pelargonin, and pelargonidin 3-O-glucoside accumulated, producing the red color [ 41 ], and at the higher DFRb-type content, petunidin 3-O-glucoside, malvidin 3-O-glucoside, delphinidin 3-O-glucoside, and cyanidin 3-O-glucoside accumulated, producing the purple color [ 42 ]. In tobacco, AN1 overexpression caused anthocyanin accumulation, leading to purple leaves.…”

Co-Expression Network Analyses of Anthocyanin Biosynthesis Genes in Ruellia (Wild Petunias; Acanthaceae)

“…Mutations occurring at these sites are more likely to impact substrate binding a nities of the corresponding enzyme resulting in new speci c interactions (Reva et al, 2011). In this study, we found multiple, orthologous copies of both F3H and DFR to be present and here hypothesizes that duplication of these genes may have facilitated functional diversi cation of the ABP in Ruellia (Huang et al, 2016).…”

“…Prior research has demonstrated lower rates of non-synonymous mutations among genes upstream in the ABP pathway compared to downstream genes (Rausher et al, 1999), likely as a function of relaxed evolutionary constraint on downstream (vs. upstream) genes (Lu and Rausher, 2003) or high rates of positive selection on downstream genes, potentially playing a role in adaptive oral color evolution (Huang et al, 2016). This pattern is expected given that upstream enzymes function in a much broader set of biosynthetic pathways (e.g., lignin and other avonoids) than downstream enzymes, which are largely speci c to anthocyanin production ( Figure S9).…”

Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants

“…Transcriptomic-based analysis has shown that the growth form and flower color-related transcription factors (MYBs) are positively selected and are possibly related to the differentiation of flower color and speciation 12 . Divergent selection and functional subdivision of anthocyanin-biosynthetic genes have also been suggested to be responsible for the rapid evolution and diversification of Scutellaria species in the island of Taiwan 13 , 14 . In addition, biogeographic analyses have indicated a very recent divergence time, within 0.2 Mya, of these two species, and their divergence was suggested to be a consequence of a series of dispersal and vicariance events corresponding to climate shifts through the late Pleistocene 15 .…”