经Horticulture Research 编委会专家评审，华北理工大学宋小明教授团队题为Flowering genes identification, network analysis and database construction for 837 plants的研究论文当选Horticulture Research 2024年4月封面文章。
Flowering is an important biological marker of the transition from vegetative growth to reproductive growth in angiosperms, and plays a central role in angiosperm growth and species evolution. The flowering process is regulated by photoperiod, low temperature induction, autonomy, biological clock, temperature, aging, hormone and glucose metabolism. A relatively comprehensive exploration of flowering genes has been carried out in the model plant Arabidopsis thaliana, but there are many flowering regulatory pathways and flowering genes involved, which makes the data collection process time-consuming and labor-intensive. Therefore, there is an urgent need to build a database platform to identify and analyze the flowering genes of many plants that have completed genome sequencing such as vegetables, and establish a comprehensive and comprehensive data sharing and analysis platform.
In this study, we collected the different flowering regulatory pathways and the flowering genes involved in the model plant Arabidopsis thaliana, and mapped the flowering gene interaction network (Fig. 1). Then, 837 high-quality genomes of vegetables and other plants were collected, and the flowering genes were identified and in-depth information comparison and analysis were carried out. In this study, we identified 80,810 genes for the photoperiod pathway, 34,373 genes for the glucose metabolism pathway, 30,396 genes for the temperature pathway, 27,451 genes for the low-temperature inducible pathway, 22,839 genes for the aging pathway, 73,286 genes for the autonomous pathway, 29,511 genes for the circadian clock pathway, 24,707 genes for the hormone pathway, and 10,155 genes for the ABCDE model. All these genes and related analysis results were stored in the "Plant Flowering Gene Database" platform (PFDB, http://pfgd.bio2db.com/) established in this study
Fig.1 Comparative analysis of flowering gene regulatory network and different taxa
At the same time, the PFGD database predicted the upstream regulatory genes of flowering genes for each species, as shown in Figure 2 of the ABCDE model. In addition, microRNAs associated with flowering genes and their target genes were identified in each species. These results provide a rich data resource for the next step of functional omics research on flowering genes in vegetables and other plants.
Fig.2 Analysis of flowering genes and their corresponding upstream regulatory genes in the ABCDE model
In addition, the PFGD database used Hi-C data to perform three-dimensional genomic analysis of flowering-related genes. Regions with distances greater than 2 Mb and high interaction intensity are indicated in red (Figure 3). Regulatory elements in the red junction region are more likely to regulate the activity of flowering genes at the three-dimensional level. These findings provide a rich data resource for functional genomics and molecular breeding research of flowering genes.
Fig.3 Cis regulatory elements related to flowering genes and their regulatory relationships in three-dimensional genomic data
Finally, a user-friendly platform for sharing and analyzing flowering gene data of vegetables and other plants, the "Plant Flowering Gene Database" (PFGD, http://pfgd.bio2db.com/) (Fig. 4), was established to provide abundant genetic resources for flowering-related researchers and breeders.
Figure 4 Framework diagram of the PFGD database platform
In summary, this is the first large-scale identification and systematic comparative analysis of flowering genes in vegetable crops and other plant genomes. The flowering gene sequences and analysis results of all species can be downloaded and used from the PFGD database built in this project. The construction of this database platform will greatly promote the functional research process of flowering genes in vegetables and other plants. It is hoped that PFGD will provide a convenient platform for researchers related to flowering genes around the world. In the future, the database will continue to focus on high-quality species with flowering genes and new sequencing, and update relevant research results.
Professor Song Xiaoming of North China University of Science and Technology is the corresponding author, and Wu Tong, a master's degree graduate (now a doctoral student of Hebei Agricultural University), and Liu Zhuo and Yu Tong, a master's student, are the co-first authors. A number of teachers and students from the innovative research team of functional genetics of vegetable crops at North China University of Science and Technology, as well as associate professor Zhou Rong of Nanjing Agricultural University, also participated in this study. This work was supported by projects such as Hebei Outstanding Youth, the National Natural Science Foundation of China, and the Natural Science Foundation of Hebei Province.
At the forefront of plant science, focusing on the frontier progress of plant science, the release of information, recruitment information and method software sharing. For submission and recruitment, please reply to "contribution" in the background, all of which are free of charge; for business cooperation, please contact WeChat ID: zwkxqy;