School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
BMC Plant Biol. 2018 Oct 26;18(1):256. doi: 10.1186/s12870-018-1437-8.
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. 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.
In 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".
We 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.
随着测序技术的快速发展，植物的比较基因组研究揭示了整个植物进化过程中反复发生的全基因组复制（即多倍化）事件。植物基因的进化历史应该在不同植物谱系中反复发生的多倍化事件的背景下进行分析。植物的血管植物一个锌指（VOZ）基因家族编码与许多重要性状相关的转录因子，包括控制开花时间和光周期途径，但这个基因家族的进化轨迹仍未被描述。
在这项研究中，我们通过整合方法：系统发育重建、基于 Ks 的年龄估计和基因组共线性比较，分析了 46 个植物基因组中的 107 个 VOZ 基因，解析了 VOZ 基因家族的进化历史。通过仔细研究 VOZ 基因家族的系统发育，很好地界定了核心真双子叶植物γ事件，并通过整合来自油棕和香蕉的基因检测到了 precommelinid τ 复制事件的遗迹。最近的 T 和 ρ 多倍化事件也被识别出来，它们分别与茄科和禾本科的物种多样化密切相关。捕获到的其他重要多倍化事件包括杨树和柳树中的“水杨酸盐”事件、大豆中的“早期豆科”和“大豆特异性”事件，以及 Physcomitrella patens 中的最近多倍化事件。虽然 VOZ 基因是一个小的转录因子基因家族，但它们的进化历史为植物中的多倍化事件提供了一个极好的记录。VOZ 基因家族的进化历史与关键的植物多倍化事件密切相关，这些事件产生了物种多样化，并为达尔文的“可恶的谜团”提供了答案。
我们解析了植物中 VOZ 转录因子家族的进化历史，并同时重构了植物的祖先多倍化事件。这种分析允许生成一个理想化的植物基因树，展示了多倍化事件后独特的保留和分裂模式。
