Additional file 2 of Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Creators: name: He, Yuqi
name: Zhang, Kaixuan
name: Shi, Yaliang
name: Lin, Hao
name: Huang, Xu
name: Lu, Xiang
name: Wang, Zhirong
name: Li, Wei
name: Feng, Xibo
name: Shi, Taoxiong
name: Chen, Qingfu
name: Wang, Junzhen
name: Tang, Yu
name: Chapman, Mark A.
name: Germ, Mateja
name: Luthar, Zlata
name: Kreft, Ivan
name: Janovská, Dagmar
name: Meglič, Vladimir
name: Woo, Sun-Hee
name: Quinet, Muriel
name: Fernie, Alisdair R.
name: Liu, Xu
name: Zhou, Meiliang
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Additional file 2: Figure S1. Nucleotide diversity of HW, SL1, SL2, NLI and NLO groups. Figure S2. FST between different groups. Figure S3. Assessment of graph model of Tartary buckwheat accessions. Figure S4. The range of estimated divergence times between the populations. Figure S5. Divergence time between HW and SL, HW and NL, SL1 and SL2, NLI and NLO groups predicted with SMC++. Figure S6. Individuals of ten mini-groups based on geographical distribution was carried out using silhouette scoring. Figure S7. Silhouette scores of individuals used for Treemix analysis was carried out using silhouette scoring. Figure S8. Evaluation of introgression components between different population. Figure S9. Gene ontology analysis and KEGG enrichment analysis of genes in selective sweeps identified in both HW vs. SL and HW vs. NL comparisons. Figure S10. Local XP-CLR plot of the locus FtGULO located. Figure S11. FtGULO phylogenetic based on the neighbor-joining method tree using full-length amino acid sequences of orthologues genes in Tartary buckwheat and other plants. Figure S12. Geographic distribution of the Hap-A and Hap-T Tartary buckwheat accessions. Figure S13. PCR analysis of Arabidopsis lines heterologously expressing FtGULO. Figure S14. Gene ontology analysis and KEGG enrichment analysis of gene in regions of selective sweeps between SL and NL. Figure S15. FtPK phylogenetic tree based on the neighbor-joining method tree using full-length amino acid sequences of orthologues genes in Tartary buckwheat and other plants. Figure S16. Frequencies of the two haplotypes in the low ECE and high ECE groups. Figure S17. Geographic distribution of the Hap-1 and Hap-2 Tartary buckwheat accessions. Figure S18. PCR analysis of Arabidopsis lines heterologously expressing FtPK. Figure S19. MDA content and POD activity in Arabidopsis heterologously expressing FtPK compared to WT with and without a salt treatment. Figure S20. Hi-C contact matrix of the high-quality chromosome-scale genome assembly of EDT. Figure S21. Collinearity among the assembly of EDT, the genetic map of the RIL population, the HERA version assembly (DDT genome used in this study) and the V2 version assembly of Tartary buckwheat variety Pinku1 reference genome. Figure S22. The distribution of deletions and insertions between EDT and DDT on eight chromosomes of Tartary buckwheat.