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Jeremy Corbyn has said he wishes Clive Lewis well and "looks forward to working with him in the future" after he resigned from the shadow cabinet.
Mr Corbyn has told Labour MPs to back the Brexit Bill at its third reading, something Mr Lewis said he could not do.
The Labour leader said: “I would like to thank Clive for his work in the shadow cabinet, which has underlined what an asset he is to the Labour Party and our movement.
“I understand the difficulties MPs representing constituencies which voted Remain have in relation to the European Union Withdrawal Bill. MPs have a duty to represent their constituents as well as their party.
“However, the Labour Party respects the outcome of the EU referendum, so we have asked all Labour MPs to vote for the Bill at its third reading tonight.
“We have been clear from the start that Labour will not frustrate the triggering of Article 50, which represents the start of the process for leaving the EU."
The MP for Norwich South, Clive Lewis, has said he quit the Shadow Cabinet with a "very heavy heart".
In his resignation letter to Jeremy Corbyn he said: "I know you understand the deep divide this issue has opened up in the country and it is to your credit that you have lead the debate in our party in such an open and comradely way."
Clive Lewis posted this picture of Star Trek's Mr Spock.
It refers to the 'no win scenario' that cadets in the United Federation of Planets must go through before becoming officers.
Our Political Reporter Emma Hutchinson got some early reaction to Clive Lewis' decision to stand down.
Mr Lewis had pledged to vote against the bill if it went through unamended. The majority of his constituency voted to remain in the EU referendum.
Norwich South MP and Shadow business secretary Clive Lewis and has resigned from the shadow cabinet in order to defy Labour leader Jeremy Corbyn's order to back the European Union (Notification of Withdrawal) Bill at third reading, its final Commons stage.
Latest ITV News reports
Former cabinet member who quit to defy Jeremy Corbyn at Brexit vote says rumours he is considering a leadership challenge are "fantasy".
The Norwich South MP Clive Lewis says he was keeping his promise to constituents when he refused to back last night's Brexit Bill.