PGCP: A comprehensive database of plant genomes for comparative phylogenomics

With the rapid advancement of sequencing and genome assembly technologies, thousands of plant genomes have been sequenced, assembled and annotated (Marks et al., 2021; Xie et al., 2024), providing a rich and invaluable resource for comparative genomic and evolutionary studies in plants. However, these genomes are often dispersed across various databases, creating barriers to efficient data access, integration and comprehensive analysis. Existing plant genome databases, such as Phytozome (Goodstein et al., 2012) and Ensembl Plants (Bolser et al., 2017), offer significant contributions but are limited in scope, typically covering only a limited number of species and a few representative genomes. The lack of a centralized platform for accessing and analysing diverse plant genomes makes it challenging to perform large-scale comparative studies, impeding the identification of conserved and divergent genomic features and hampering the discovery of broader evolutionary and functional patterns across the plant kingdom. Therefore, there is a pressing need for a comprehensive, user-friendly and integrative database that brings together high-quality genomic data from a wide range of plant species. Here, we introduce PGCP (Plant Genomes for Comparative Phylogenomics), a comprehensive database that integrates extensive genomic data across the plant phylogeny. PGCP consolidates 719 publicly available genomes from various platforms and published studies, ensuring the inclusion of high-quality assemblies and complete annotation information (Figure 1a). After rigorous quality control, we obtained a total of 26 600 642 protein-coding genes from these genomes. To enhance data consistency and usability, we performed a uniform and standardized re-building of genome annotations across the database. Gene and chromosome identifiers (IDs) were transformed into PGCP-specific identifiers, with records carefully filtered to maintain data integrity and confidentiality. All the protein-coding genes were further annotated with various functional attributes, including the prediction of transcription factors (TFs) and transcriptional regulators (TRs), using iTAK (Zheng et al., 2016). Additionally, gene ontology (GO) terms and protein domain annotations were assigned using InterProScan (Jones et al., 2014), providing a comprehensive functional landscape of the gene datasets (Figure 1b). To uncover hidden patterns within extensive genomic datasets, we conducted a large-scale comparative phylogenomic analysis using OrthoFinder (Emms and Kelly, 2019). From the 719 genomes collected in PGCP, we identified 237 400 orthogroups, each comprising genes from at least three different species. This comprehensive resource enables the exploration of complex evolutionary relationships by comparing homologous genes across plant species, tracing gene family origination and divergence that highlight adaptive evolution, identifying lineage-specific genes contributing to unique species characteristics and predicting gene functions based on conserved and divergent features (Figure 1c). Such analyses provide an in-depth understanding of the genetic foundations of plant diversity, offering valuable information on evolutionary trajectories, adaptive strategies and functional innovations in the plant kingdom. In a nutshell, the integration of these orthogroups significantly enhances the utility of the PGCP database, making it an invaluable resource for advancing evolutionary research. In summary, PGCP aims to provide an extensive and accessible platform that integrates genomic data across a wide array of plant species, encompassing well-studied model plants, important crops and diversified wild plants. By offering a unified repository of high-resolution genome sequences, annotations and comparative genomics data, PGCP facilitates large-scale comparative analyses and enables researchers to explore plant phylogenetics, gene family dynamics and functional genomics across the plant kingdom. The database includes advanced analytical tools that support the identification of homologues, phylogenetic reconstruction and the discovery of key genes involved in adaptive and agronomic traits. As a unified platform, PGCP is designed to be an essential resource for researchers in plant biology, fostering new insights into plant evolution, biodiversity and the molecular mechanisms that drive trait diversity. In the future, we plan to expand the PGCP database by incorporating additional plant genome resources to enhance its comprehensiveness. As part of our ongoing development, we will work towards systematically including genomes from GWH (Ma et al., 2025) and other relevant databases to provide a more extensive and up-to-date resource for the plant research community. This work is supported by the National Natural Science Foundation of China (No. 32070656 to D.C. and 32070243 to Z.-Q.S.) and the Fundamental Research Funds for the Central Universities (to J.-Y.X.). The authors acknowledge the Center for Information Technology and the High-Performance Computing Center of Nanjing University for providing high performance computing (HPC) resources. D.C., J.-Y.X. and Z.-Q.S. conceived and supervised the study. H.-Y.F., X.-Y.F. and X.Z. collected genome sequence, gene annotation and meta data with help from J.Y., Q.H. and Y.Y. X.Z. and Z.R. processed the genomic data and constructed the database with support from H.C. and M.C. D.C. wrote the manuscript. All authors reviewed and approved the submitted manuscript. The authors declare no competing interests. The PGCP database is available at https://biobigdata.nju.edu.cn/PGCP/.