OGRP: A comprehensive bioinformatics platform for the efficient empowerment of Oleaceae genomics research

Zijian Yu; Yu Li; Tengfei Song; Lixia Gou; Jiaqi Wang; Yue Ding; Zejia Xiao; Jingyue Qin; Hui Jiang; Yan Zhang; Yishan Feng; Xiangming Kong; Shoutong Bao; Shouliang Yin; Tianyu Lei; Jinpeng Wang

Horticultural Plant Journal (May 2025)

OGRP: A comprehensive bioinformatics platform for the efficient empowerment of Oleaceae genomics research

Zijian Yu,
Yu Li,
Tengfei Song,
Lixia Gou,
Jiaqi Wang,
Yue Ding,
Zejia Xiao,
Jingyue Qin,
Hui Jiang,
Yan Zhang,
Yishan Feng,
Xiangming Kong,
Shoutong Bao,
Shouliang Yin,
Tianyu Lei,
Jinpeng Wang

Affiliations

Zijian Yu: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Yu Li: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Tengfei Song: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Lixia Gou: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Jiaqi Wang: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Yue Ding: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Zejia Xiao: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Jingyue Qin: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Hui Jiang: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Yan Zhang: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Yishan Feng: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Xiangming Kong: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Shoutong Bao: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
Shouliang Yin: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China; Corresponding authors.
Tianyu Lei: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding authors.
Jinpeng Wang: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China; Corresponding authors.

Journal volume & issue: Vol. 11, no. 3
pp. 1308 – 1325

Abstract

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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, 1 952 225 collinear gene pairs, multiple genome alignments, and imprints of paleochromosome rearrangements. Moreover, in Oleaceae genomes, researchers can efficiently search for 1 785 987 functional annotations, 22 584 orthogroups, 29 582 important trait genes from 74 gene families, 12 664 transcription factor-related genes, 9 178 872 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.

Published in Horticultural Plant Journal

ISSN: 2095-9885 (Print); 2468-0141 (Online)
Publisher: KeAi Communications Co., Ltd.
Country of publisher: China
LCC subjects: Agriculture: Plant culture
Website: https://www.keaipublishing.com/en/journals/horticultural-plant-journal/

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