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

Bei Gao,Andrew J Wood,Xiaoshuang Li,Melvin J Oliver,Fuyuan Zhu,Yuqing Liang,Moxian Chen,Tieyuan Liu,Jianhua Zhang,Daoyuan Zhang

doi:10.1186/s12870-018-1437-8

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.

Highlights

Facilitated by the rapid progress of sequencing technology, comparative genomic studies in plants have unveiled recurrent whole genome duplication events throughout plant evolution
As recorded in PlantTFDB [57], Vascular Plant One Zinc-finger (VOZ) transcription factors are restricted to the land plants and originally emerged in the genomes of bryophytes but are absent in the liverwort Marchantia polymorpha (Marchantiophyta) and the lycophyte Selaginella moellendorffii (Lycopodiophyta), which was validated by whole genome homolog sequence searches
Phylogenetic analyses, Synonymous substitutions per synonymous site (Ks)-based molecular dating and genome synteny network centered on the VOZ gene family provided consistent and robust evidence supporting the hypothesis that VOZ gene family members were products of the γ and T events in core-eudicots, the pre-commelinid τ and grass-wide ρ events in monocots, and the “recent” Whole Genome Duplication (WGD) events in the moss Physcomitrella patens (Fig. 8)

Summary

Introduction

Facilitated 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. In the eudicots, representing over 75% of extant angiosperms, the γ whole genome triplication event occurred around 117 Mya and is associated with the early diversification of the core eudicots. Based on age distributions and chromosome structural analyses with fully sequenced genomes, a series of recurrent polyploidy events have been identified [5, 8]. Both potato and tomato genomes contained evidence for a common Solanum whole genome triplication event (termed T) and formed the T-γ polyploidization series in Solanum [18, 19]. The lotus-specific λ WGD event occurred about 65 Mya and its genome lacks the footprint of the γ hexaploidy event [20]

Methods

Results

Discussion

Conclusion