Certain questions about pangene

[shengxinzhuan]

Hello,Prof. Li! I have carefully read the preprint of pangene and the documentation, but I still have some questions I would like to ask you.

1. Can pangene handle species that have experienced chromosomal breakage and fusion, such as in plants where the fusion of a genus's species is very common? In this case, can pangene provide the range of breakpoints, or will it simply be lost? As I know, in the cactus-minigraph workflow based on genome alignment, this part will be directly removed.
2. For species that have undergone different whole-genome duplication events, is there a corresponding method to construct the gene set of this clade? If so, this would be a very nice idea for understanding the gene loss and gain in species.