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

Authors: GAO, BEI - The Chinese University Of Hong Kong (CUHK); CHEN, MOXIAN - The Chinese University Of Hong Kong (CUHK); LI, XIAOSHUANG - Chinese Academy Of Sciences; LIANG, YUQING - Chinese Academy Of Sciences; ZHU, FUYUAN - The Chinese University Of Hong Kong (CUHK); LIU, TIEYUAN - The Chinese University Of Hong Kong (CUHK); ZHANG, DAOYUAN - Chinese Academy Of Sciences; WOOD, ANDREW - Southern Illinois University; Oliver, Melvin; ZHANG, JIANHUA - The Chinese University Of Hong Kong (CUHK)

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2018
Publication Date: 10/26/2018
Publication URL: http://handle.nal.usda.gov/10113/6178696
Citation: Gao, B., Chen, M., Li, X., Liang, Y., Zhu, F., Liu, T., Zhang, D., Wood, A.J., Oliver, M.J., Zhang, J. 2018. Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors. Biomed Central (BMC) Plant Biology. 18:256. https://doi.org/10.1186/s12870-018-1437-8.
DOI: https://doi.org/10.1186/s12870-018-1437-8

Interpretive Summary: In order to fully understand how plants have adapted to different environments and large-scale events, it is important to determine how plant genomes have evolved over time. Of particular interest are the whole genome duplication events that resulted in large "bursts" of species diversity at specific times in the earth's history. These events are thought to play a role in adaptation to changing environments. We used a specific transcription factor gene, the VOZ gene, a gene that controls the expression of flowering time in plants to follow the evolution of plant genomes. By analyses of 107 VOZ genes in 46 plant families using integrated computational methods and genome region characterizations we were able to detect the core duplication events that have been reported for plant genomes as well several new events that have occurred in specific plant lineages, including ones in the grasses and in soybean lineages. The stringent correlation between the evolution of the VOZ gene family with critical plant polyploidy (genome duplication) allowed for the generation of an idealized plant gene tree demonstrating distinctive retention and fractionation patterns following major whole genome events. This research helps to inform our efforts to adapt plants to changing environments and should help to direct efforts for crop improvement.

Technical Abstract: 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. We deciphered the evolutionary history of the Vascular Plant One Zinc-finger (VOZ) gene family by analyses of 107 VOZ genes in 46 plant genomes using integrated methods: phylogenic reconstruction, Ks-based age estimation and genomic syntenic comparisons. The VOZ gene family encode transcription factors associated with a number of important traits including control of flowering time and photoperiodic pathways. Using an outgroup minus method the core eudicot ' event was well circumscribed, and the precommelinid t duplication event was detected by incorporating genes from oil palm and banana. The more recent T and ' polyploidy events, closely coincident with the species diversification in Solanaceae and Poaceae respectively, were also identified. Other important polyploidy events identified included the “salicoid” in populus and willow, and “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 stringent correlation between the evolution of the VOZ gene family with critical plant polyploidy events which generated species diversification and established the origin of flowering plants and the answer to Darwin’s “abominable mystery”. Furthermore, we propose that part of the VOZ gene originated from a region of a bacterial excinuclease ABC subunit A by homolog detection. This analysis allowed for the generation of an idealized plant gene tree demonstrating distinctive retention and fractionation patterns following polyploidy events.