Same gene in multiple orthogroups

[jacopoM28]

Hello all,

I am using GENESPACE to identify syntenic and non-syntenic orthologs between three species. After running the 'query_pangenome' function, I noticed that the same gene could be present across multiple orthogroups, in both syntenic and non-syntenic relationships. Is this expected? Here is one example where a Tlat gene has two orthologues relathionships:

pgID      interpChr interpOrd    og      repGene        genome    chr   start     end Msex_peptides Tlat_peptides Vcon_peptides
<int>         <char>     <num> <int>       <char>        <char>     <char>   <num>   <num>        <list>        <list>     <list>   
196 NW_025408616.1       174  3968 H6S33_000174 Msex_peptides   NW_025408616.1  686601  689222  H6S33_000174   FUN_002804*    jgi_Vercon1_465788
5271 NW_025408621.1      4539  1785 H6S33_011584 Msex_peptides   NW_025408621.1 1785762 1788327  H6S33_011584    FUN_002804    jgi_Vercon1_403145

Best,
Jacopo