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

About germplasm & population

The "population" module includes 161 O. fragrans plant accessions from china, we provide the cultivar, geographic distribution, subgroup, and depth and coverage of resequencing for each plant. The 161 O. fragrans accessions were categorized into four subgroups: 73 "Yingui" group, 38 "Jingui" group, 22 "Sijigui" group, and 28 "Dangui" group and distributed in four regions of China: 6 Guangxi province, 19 Hubei province, 45 Sichuan province, and 48 Zhejiang province. The average depth and coverage of resequencing of 161 O. fragrans accessions were 16.97x and 92.34%, respectively [1].

All resequencing reads of the 161 O. fragrans accessions were mapped to the O. fragrans "Liuyejingui" reference genome. SNP calling was performed using the Genome Analysis Toolkit (v4.1.4.1) [2]. The SNPs in the joint genotyping were further filtered to remove SNP sites with MAF < 0.05, sequencing depth < 4, and those that had samples with missing data. Tag SNPs were selected using PLINK (v.1.90) [3] with parameter "-blocks" to construct neighbour-joining tree. The neighbour-joining tree was constructed using TreeBeST (v.1.9.2) [4] software with 1,000 replicates of bootstrap. PCA of all SNPs were performed using genome-wide complex trait analysis (GCTA) (v.1.91.7) [5] software with default parameters. We also investigated the population structure using ADMIXTURE (v1.3.0) [6].

To explore the candidate regions potentially effected by selection, we calculated nucleotide diversity (π) and population fixation statistics (FST). π was calculated with expected heterozygosity per site derived from the average number of sequence differences in four subgroups ("Yingui", "Jingui", "Sijigui", and "Dangui") using VCFtools (v0.1.17) in a 500-kb sliding window with a step size of 50 kb [7]. FST, which indicates genomic differentiation between subgroups, was calculated for each pair of subgroups using VCFtools in a same windows size as that of π. The outlier of FST were determined as windows with the top 5% of FST values, indicating divergent selection of the regions.

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. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20:1297-1303.
  3. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575.
  4. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19:327-335.
  5. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011, 88:76-82.
  6. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009, 19:1655-1664.
  7. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics 2011, 27:2156-2158.