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Constructing a pangenome gene graph
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Certain questions about pangene #6

Open shengxinzhuan opened 5 months ago

shengxinzhuan commented 5 months ago

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.