Phylogenetic analysis
The phylogenetic relationships between Chinese flowering cabbage and
other Brassica plants were analyzed using the orthologs from
single-copy genes. The Orthofinder package was used to find orthogroups
and single-copy genes. All of the single-copy genes in one species were
concatenated into a super alignment, then run through multiple sequence
alignment using the mafft
program(Katoh & Toh,
2010). Easyspecietree (https://github.com/Davey1220/EasySpeciesTree)
was used to generate the phylogenetic relationship between the species
using the maximum likelihood method.