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Israel killed several top Iranian commanders and nuclear scientists on June 13 at the start of the war.
Khamenei's remarks come two days after a ceasefire ended a 12-day war between Iran and Israel, the foes' deadliest and most destructive confrontation in history.
Trump said Iranian officials had reached out about negotiations, including a possible meeting at the White House, but "it's very late to be talking," he said.
The US president has so far stressed that his country is not getting involved in the conflict, and has said that Iran could still take a deal to end its nuclear program that he had proposed before Israel's attacks.
The Israeli military said Shadmani had commanded both the Islamic Revolutionary Guard Corps and the Iranian armed forces.
Netanyahu did not reveal whether or not Israel was targeting the Ayatollah.
Ayatollah Ali Khamenei made the remark about Indian Muslims in his message to the community, stressing unity, on the occasion of Prophet Mohammed’s birth anniversary.
In Iran's first official reaction to Friday's attack, ministry spokesperson Nasser Kanaani said freedom of speech did not justify Rushdie's insults against religion.
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