As a high-value eudicot family, many famous horticultural crop genomes have been deciphered in Oleaceae. However, there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae. Herein, we developed the first comprehensive Oleaceae Genome Research Platform (OGRP, https://oleaceae.cgrpoee.top/). In OGRP, 70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained. We built 34 window-operated bioinformatics tools, collected 38 professional practical software programs, and proposed 3 new pipelines, namely ancient polyploidization identification, ancestral karyotype reconstruction, and gene family evolution. Employing these pipelines to reanalyze the Oleaceae genomes, we clarified the polyploidization, reconstructed the ancestral karyotypes, and explored the effects of paleogenome evolution on genes with specific biological regulatory roles. Significantly, we generated a series of comparative genomic resources focusing on the Oleaceae, comprising 108 genomic synteny dot plots, 1952225 collinear gene pairs, multiple genome alignments, and imprints of paleochromosome rearrangements. Moreover, in Oleaceae genomes, researchers can efficiently search for 1785987 functional annotations, 22584 orthogroups, 29582 important trait genes from 74 gene families, 12664 transcription factor-related genes, 9178872 transposable elements, and all involved regulatory pathways. In addition, we provided downloads and usage instructions for the tools, a species encyclopedia, ecological resources, relevant literatures, and external database links. In short, ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating, which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research, including evolution, genetics, genomics, ecology, agriculture, forestry, and global climate. To investigate which plant conserves best the core eudicots common ancestor genome, we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families. The genomes of Davidia involucrata (a known living fossil), Camptotheca acuminata and Nyssa sinensis, one per existent genus of Nyssaceae, were performed comparative genomic analysis. We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event (NCT)– autotetraploidization 28–31 Mya after the core eudicot common hexaploidization (ECH). We identified Nyssaceae orthologous and paralogous genes, determined its chromosomal evolutionary trajectory, and reconstructed the Nyssaceae most recent ancestor genome. D. involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families. Combing both its high retention of paleochromosomes and its low mutation rate, D. involucrata provides the best case in conservation of the core eudicot paleogenome.