hi,
switchport trunk allowed vlan 1,50-89 - this command identifies which VLANs should pass through the trunk across to the other switch
switchport trunk native vlan 1 - this command identifies which untagged VLAN will cross the trunk. 802.1Q trunk by default uses VLAN 1 as the native VLAN
bonding interface - i think you're referring to etherchannel.