Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors

Abstract

BackgroundFacilitated by the rapid progress of sequencing technology, comparative genomic studies in plants have unveiled recurrent whole genome duplication (i.e. polyploidization) events throughout plant evolution. The evolutionary past of plant genes should be analyzed in a background of recurrent polyploidy events in distinctive plant lineages. The Vascular Plant One Zinc-finger (VOZ) gene family encode transcription factors associated with a number of important traits including control of flowering time and photoperiodic pathways, but the evolutionary trajectory of this gene family remains uncharacterized.ResultsIn this study, we deciphered the evolutionary history of the VOZ gene family by analyses of 107 VOZ genes in 46 plant genomes using integrated methods: phylogenic reconstruction, Ks-based age estimation and genomic synteny comparisons. By scrutinizing the VOZ gene family phylogeny the core eudicot γ event was well circumscribed, and relics of the precommelinid τ duplication event were detected by incorporating genes from oil palm and banana. The more recent T and ρ polyploidy events, closely coincident with the species diversification in Solanaceae and Poaceae, respectively, were also identified. Other important polyploidy events captured included the “salicoid” event in poplar and willow, the “early legume” and “soybean specific” events in soybean, as well as the recent polyploidy event in Physcomitrella patens. Although a small transcription factor gene family, the evolutionary history of VOZ genes provided an outstanding record of polyploidy events in plants. The evolutionary past of VOZ gene family demonstrated a close correlation with critical plant polyploidy events which generated species diversification and provided answer to Darwin’s “abominable mystery”.ConclusionsWe deciphered the evolutionary history of VOZ transcription factor family in plants and ancestral polyploidy events in plants were recapitulated simultaneously. This analysis allowed for the generation of an idealized plant gene tree demonstrating distinctive retention and fractionation patterns following polyploidy events.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1437-8) contains supplementary material, which is available to authorized users.

Expression Analyses of Soybean VOZ Transcription Factors and the Role of GmVOZ1G in Drought and Salt Stress Tolerance

“…Since the VOZ transcription factor was first reported [15], studies on its expression and functional validation were mainly concentrated on the model plant, Arabidopsis, but other species have rarely been investigated. Six VOZ transcription factors were demonstrated to exist in the soybean genome [25]. According to the Plant Transcriptional Regulatory Map (PlantRegMap) database [26], the VOZ transcription factor family has more members in soybean than in many other species, which suggests that soybean VOZ transcription factors may have more complex functions and participate in more regulatory mechanisms.…”

“…Six soybean VOZ genes were annotated and designated as GmVOZ1A, GmVOZ1C, GmVOZ1E, GmVOZ1G, GmVOZ2B, and GmVOZ2D [25]. To elucidate the evolutionary history of soybean VOZ genes and their phylogenetic relationship with VOZ family genes in other organisms, VOZ proteins from five other plant species, Arabidopsis, rice, maize, foxtail millet, and P. patens, were aligned, and then a phylogenetic tree was constructed ( Figure 1).…”

Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses

“…Compared to conventional gene family studies that focus on one or a limited number of species of interest(Kalluri et al , 2007, Wang et al , 2007, Wang et al , 2012b), phylogenetic studies on a broader scale that include multiple plant lineages were able to generate a more robust insights into the evolutionary process that gave rise to the modern assemblage of a target gene family (Finet et al , 2013, Li et al , 2015). The inclusion of genomic synteny data provides important information that impacts the determination of the evolutionary past of a gene family, especially when the gene family of interest evolved in parallel with ancestral genome duplication events (Gao et al , 2018). The conventional genomic block alignment that connects orthologues, retained on genomic syntenic blocks, worked well for a limited number of species(Cheng et al , 2013, Gao et al , 2018), but a network approach was more effective when multiple genomes were included in the synteny analyses(Zhao et al , 2017, Zhao and Schranz, 2017).…”

“…The inclusion of genomic synteny data provides important information that impacts the determination of the evolutionary past of a gene family, especially when the gene family of interest evolved in parallel with ancestral genome duplication events (Gao et al , 2018). The conventional genomic block alignment that connects orthologues, retained on genomic syntenic blocks, worked well for a limited number of species(Cheng et al , 2013, Gao et al , 2018), but a network approach was more effective when multiple genomes were included in the synteny analyses(Zhao et al , 2017, Zhao and Schranz, 2017). A comprehensive genomic synteny network can be constructed using nodes to represent the target genes and associated adjacent genomic blocks and the network edges (connecting lines) to represent syntenic relationships(Zhao and Schranz, 2017, Gao et al , 2018).…”

“…The conventional genomic block alignment that connects orthologues, retained on genomic syntenic blocks, worked well for a limited number of species(Cheng et al , 2013, Gao et al , 2018), but a network approach was more effective when multiple genomes were included in the synteny analyses(Zhao et al , 2017, Zhao and Schranz, 2017). A comprehensive genomic synteny network can be constructed using nodes to represent the target genes and associated adjacent genomic blocks and the network edges (connecting lines) to represent syntenic relationships(Zhao and Schranz, 2017, Gao et al , 2018). The recently established phylogenomic synteny network methodology was able to integrate and summarize genomic synteny relationships to uncover and place genomic events (e.g.…”