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Guareschi left his Ducati position to head up Rossi's first foray into team management in the third-tier world championship class this year.
He will be replaced by long-time Rossi associates Alessio Salucci and Carlo Alberto Tebaldi.
Rossi created his team as a springboard for young Italian riders, and is running Romano Fenati and Francesco Bagnaia in 2014
Fenati was in title contention at the start of the year, but since winning the team's home event at Mugello in June, his form has declined.
He has failed to make it into the top 10 at four of the last six events, finishing just outside the points in 16th at Silverstone last weekend, amid rumours in the Italian press of tensions within the team.
Fenati has consequently fallen to fifth in the championship, 44 points behind leader Jack Miller, whose main rival is now MotoGP world champion Marc Marquez's younger brother Alex.
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