Overview

Welcome to OGRP

OGRP (Oleaceae Genome Research Platform) is a comprehensive and user-friendly platform designed for the functional genomics study of the Oleaceae. it is easy to obtain the 70 genomes of ten species in Oleaceae and 46 eudicots, as well as 366 transcriptomes involving 18 tissues of Oleaceae plants. We built 34 window operated bioinformatics tools (WOBTs), collected 38 professional practical software, and proposed three new pipelines: ancient polyploidization identification (API), ancestral karyotype reconstruction (AKR), and gene family evolution (GFE). Significantly, we generated a series of comparative genomic resources focusing on the Oleaceae, including 108 genomic synteny dotplots, 1,952,225 collinear gene pairs, multiple genome alignments, and imprints of paleochromosome rearrangements. Moreover, researchers can efficiently search for 1,785,987 functional annotations, 22,584 orthogroups, 29,582 important trait genes from 75 gene families, 12,664 transcription factor related genes, 9,178,872 transposable elements, and all involved regulatory pathways in Oleaceae genomes.

OGRP Portals

70

Genomic data

366

Transcriptome

23,647

Hierarchical alignments

23,968

Event-related genes

29,582

Functional genes

12,664

Transcription factors

151

Species information

20,861

References

22,584

Orthologous

162,692

Duplication
type

9,178,872

Transposable elements

1,785,987

Gene annotations

Genomic analysis pipelines

Genome Data (70)

Species Name Genome Version Genome Access Genome Size (Mb) Assembly Level Provenance
Forsythia suspensa Forsythia-HENAU2018 GCA_013103335.1 737.5 Contig ➠
Forsythia suspensa JALRMA01 GCA_020510225.1 737.6 Chromosome ➠
Forsythia suspensa JAHHPY01 GCA_023638005.1 737.5 Chromosome ➠
Fraxinus americana FRAX14-0.1 GCA_903798225.1 642.6 Scaffold ➠
Fraxinus excelsior FRAX_001 GCA_019097785.1 806.5 Chromosome ➠
Fraxinus excelsior BATG-0.5 GCA_900149125.1 867.5 Scaffold ➠
Fraxinus pennsylvanica version 1.5 GCA_912172775.2 756.8 Chromosome ➠
Fraxinus pennsylvanica FRAX09-0.1 GCA_903798245.1 902.5 Scaffold ➠
Fraxinus pennsylvanica FRAX03-0.1 GCA_902829185.1 700.9 Contig ➠
Fraxinus pennsylvanica FRAX10-0.1 GCA_902829155.1 761 Contig ➠
Jasminum sambac Hutoumoli GCA_018223645.1 505.5 Chromosome ➠
Jasminum sambac Single-petal GWHBFHK00000000 502.3 Chromosome ➠
Jasminum sambac Double-petal GWHBFHJ00000000 487 Chromosome ➠
Jasminum sambac ... GWHAZHY00000000 550 Chromosome ➠
Jasminum sambac JSU-FSP GWHBISM00000000 500.6 Chromosome ➠
Jasminum sambac Hutou GWHDUBQ00000000 469.5 Chromosome ➠
Olea europaea O_europaea_v1 GCA_002742605.1 1126.4 Chromosome ➠
Olea europaea Farga GCA_902713445.1 1331.2 Chromosome ➠
Olea europaea YAF_Ocus_V1 GCA_023089605.1 1228.8 Chromosome ➠
Olea europaea OE6 GCA_900603015.1 1331.2 Scaffold ➠
Osmanthus fragrans Liuyejingui GCA_019395295.1 733.3 Chromosome ➠
Syringa oblata IBSOV1 GWHBHRY00000000 1146.9 Chromosome ➠
More ... ... ... ... ...

Citation

If you use OGRP in your scientific research, please cite us:

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

Update log

  • June. 20, 2024   Built the JBrowse module to visualize transcriptome data.

  • May. 8, 2024   Implemented the ability to obtain genes based on defined regions

  • May. 1, 2024   Implemented a function to draw heat maps of expression quantities

  • Nov. 10, 2023   The "Karyotype animation", which can show the evolutionary trajectory of Oleaceae karyotypes, is now available

  • Nov. 10, 2023   The "Gene function annotation", which is a gene annotation tool that allows the annotation of multiple databases in a single run, is now available

  • Nov. 10, 2023   The "KEGG database", which can show a collection of manually drawn pathway maps representing the molecular interaction, is now available

  • Nov. 8, 2023   The "Transposable elements", also known as jumping genes, is now available

  • Nov. 7, 2023   The "Transcription factors", also known as trans-acting factor, is now available

  • Nov. 5, 2023   The "Duplication type", which can divide all genes into 5 categories according to the replication type, is now available

  • Nov. 7, 2022   The "Event-related genes", which can search multiple sets of event related genes, is now available

  • Nov. 6, 2022   The "Hierarchical alignments", which can show multi genomes collinear gene table, is now available

  • Nov. 6, 2021   The "Blast visualization", which can search function annotation and position, is now available

  • Dec. 27, 2020   The "Circle" has been updated

  • May. 7, 2020   The "P-index", which can show collinearity in macro-region, is now available

  • Apr. 15, 2020   The "specie_tree", which can show collinearity in micro-region, is now available

  • Nov. 6, 2020   The "Dotplot", which can search function annotation and position, is now available