Chromosomal structure variations and GO enrichment analysis
We conducted genome-wide synteny analysis between P. tomentosaand P. trichocarpa , and subgenome synteny analysis between subgenome A and subgenome D in P. tomentosa using MCScanX (Y. Wang et al., 2012). Genome-wide structural variations (insertion, INS; deletion, DEL; inversion, INV; translocation, TRANS; copy number variation, CNV) between corresponding chromosome pairs in subgenomes were detected using MUMmer, and chromosome structural variation (SV) was identified using SVMU (Structural Variants from MUMmer) 0.3 (https://github.com/mahulchak/svmu). We extracted GO annotation data of genes mapping to the SV regions, and performed futher GO enrichment analysis. Annotation results were summarized through the mapping to the Plant GOSlim.