President Hassan Sheikh Mohamud has called a meeting of regional leaders.
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Rift comes after Somaliland deal giving landlocked Ethiopia access to the Red Sea.
Mogadishu also shuts down Addis Ababa’s consulates in Hargeisa, capital of the Somaliland, and Garowe in Puntland.
The 35 men are to be prosecuted for the hijacking of cargo vessel MV Ruen in December when they took the crew hostage.