OfIR: Osmanthus fragrans information resource
————A Multiomics Database for Osmanthus fragrans biological study
e.g. ACS1 or AT1G02970

About genomics

In the "genomics" module, we collected two published O. fragrans genomes "Liuyejingui"(OFL) [1] and "Rixianggui"(OFR) [2] and annotated the gene function, domains, metabolic pathways of genes in each genome. The gene ID, position, function annotation and homologous in Arabidopsis thaliana can be obtained in "Gene search" module. Totally, 86,794 genes of 2 O.fragrans genome assemblies were used to construct the gene index. Gene synteny of every pairs from 2 genome assemblies were detected by McScanX [3]. Gene cluster were generated based on the homologous with Arabidopsis thaliana. The "Gene family" module provided the detail gene family information of 13,730 genes in "Liuyejingui" reference genome.

We also added the interactive Scalable Vector Graphics (SVG) to exploring genes involved in different KEGG pathway (https://www.genome.jp/kegg/). Genomic synteny was constructed based on the genome alignment using Mummer, user can browse local alignment by GBrowser [4]. According to the PlantTFDB [5], the information of 56 TF families in "Liuyejingui" reference genome is provided in "Transcription factor (TF)" module.

References

  1. Chen H, Zeng X, Yang J, Cai X, Shi Y, Zheng R, et al. Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. Hortic Res 2021, 8:98.
  2. Yang X, Yue Y, Li H, Ding W, Chen G, Shi T, et al. The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans. Hortic Res 2018, 5:72.
  3. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 2012, 40:e49-e49.
  4. McKay SJ, Vergara IA, Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics 2010, Chapter 9:Unit 9 12.
  5. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 2017, 45:D1040-D1045.