Additional file 2 of Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes
Creators: name: Li, Danqing
name: Lin, Han-Yang
name: Wang, Xiuyun
name: Bi, Bo
name: Gao, Yuan
name: Shao, Lingmei
name: Zhang, Runlong
name: Liang, Yuwei
name: Xia, Yiping
name: Zhao, Yun-Peng
name: Zhou, Xiaofan
name: Zhang, Liangsheng
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. Genome-wide analysis of chromatin interactions in the Cinnamomum camphora genome using Hi-C data. Fig. S2. The genome size estimation of Cinnamomum camphora by flow cytometric analysis. Fig. S3. Synteny analysis between Cinnamomum camphora genome assembly in this study and those in published studies. Fig. S4. Syntenic comparison between Cinnamomum camphora and C. kanehirae. Fig. S5. Structural variations between Cinnamomum camphora and C. kanehirae.Fig. S6. The jackknife test of variable importance for Cinnamomum camphora and C. kanehirae. Fig. S7. Pfam analyses between Cinnamomum camphora and C. kanehirae. Fig. S8. Weighted gene co-expression network analysis (WGCNA) of the transcriptomes. Fig. S9. Coexpression network of a gene in the circadian rhythm pathway (RON3, Ccam01g03083). Fig. S10. Phylogenetic tree of cold shock protein (CSP) gene family. Fig. S11. Top 20 significantly expanded orthogroups in Cinnamomum camphora sorted by gene count ratio between C. camphora and C. kanehirae. Fig. S12. The analyses of genes under positive selection between Cinnamomum camphora and its closely related species. Fig. S13. Expression patterns of CYP450 genes in different organs and cold acclimation treatments. Fig. S14. Co-expression network analysis based on a highly expressed CYP450 gene member (Ccam02g00082). Fig. S15. Tandemly duplicated genes in Cinnamomum camphora are extremely significantly enriched in phenylpropanoid, flavonoid, and lignin-related pathway. Fig. S16. Top 20 enriched GO terms in molecular function of tandem-duplicated genes in Cinnamomum camphora. Fig. S17. Top 50 metabolites with highest contents in leaf, stem, and flower of Cinnamomum camphora. Fig. S18. Transcriptome analyses of differentially expressed genes (DEGs) with different cold treatments. Fig. S19. Gene expression in the phenylpropanoid metabolic pathway indicates the contribution to cold tolerance in Cinnamomum camphora. Fig. S20. Phylogenetic analysis and copy numbers in subfamilies of terpenoid biosynthesis genes (TPSs) during flowering plant evolution. Fig. S21. TPS-related WGCNA module and GO enrichment of TPS co-expression genes. Fig. S22. Volatile compound identification in leaf and stem of Cinnamomum camphora by GC-MS analysis. Fig. S23. Expression levels of terpenoid biosynthesis genes (TPSs) in the leaves, stems, and flowers of Cinnamomum camphora.Fig. S24. Terpenoid biosynthesis gene characterization in Cinnamomum camphora. Fig. S25. The phylogenetic tree constructed by representative single nucleotide polymorphisms (SNPs) obtained from Chr 1 of 75 resequencing Cinnamomum camphora accessions using C. kanehirae as the outgroup. Fig. S26. The species tree based on amino acid sequences of identified single-copy orthogroups (OGs) with a coalescent-based method from 22 samples with Cinnamomum kanehirae as the outgroup. Fig. S27. Functional comparison analyses of Cinnamomum camphora genomes with high quality.