$ perl -nE '/([^\(]+)\((.*)\)/ and $1 ne $2 and ++$seen{$2} < 2 and say "$1 : $2"' raw_data.txt
Metan1_4283 : Metac1_3189
MagorCD156_00067621 : MagorUS71_00075311
Phaca1_206503 : Phchr2_2932727
Thite2_36710 : Thiar1_121068
Spoth2_47778 : Thiar1_767720
Micmi1_311120 : Micmi1_478558
Micmi1_478558 : Micmi1_311120