Comparative genomics, microsynteny, ancestral state reconstruction and selection pressure analysis across distinctive genomes and sub-genomes of Brassicaceae for analysis of evolutionary history of VQ gene family.

Abstract

Any unfavorable condition that affects the metabolism, growth, or development of plants is considered plant stress. The molecular response of plants towards abiotic stresses involves signaling to cellular components, repressing transcription factors, and subsequently induced metabolic changes. Most valine-glutamine (VQ) motif-containing genes in plants encode regulatory proteins that interact with transcription factors and modulate their activity as transcription regulators. Several VQ proteins regulate plant development and stress responses. In spite of the functional importance of VQs, there is relatively little information about their evolutionary history in Brassicaceae or beyond. Brassicaceae is characterized by paleoploidy, mesopolyploidy, and neopolyploidy, offering a resource for studying evolution and diversification. In current study we performed phylogeny of the VQ gene family along with comparative genomics, microsynteny and evolutionary rates analysis across seven species of Brassicaceae. Our findings revealed the following; (1) a large segmental duplication in the shared common ancestor of the family Brassicaceae, resulted in paralogies of VQ1-VQ10, VQ15-VQ24, VQ16-VQ23, VQ17-VQ25, VQ18-VQ26, VQ22-VQ27; (2) chromosomal mapping revealed diverse distributions of the gene family; (3) duplicated segments undergo varying degrees of retention and loss; and (4) Out of the 12 paralogous members, most of the genes are under purifying selection. However, VQ23 in Brassicaceae stands out as it is under positive selection, indicating the need for further investigation. Overall, our results clearly establish that the ancestral VQ1/VQ10, VQ15/VQ24, VQ16/VQ23, VQ17/VQ25, VQ18/VQ26, VQ22/VQ27 genes duplicated in shared common ancestor of Brassicaceae.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-023-01347-z.