Shami, who last played a one-day global in the 2015 World Cup, has recovered from injury and been playing with the Delhi Daredevils in the Indian Premier League. Rohit Sharma and Ajinkya Rahane are the other two.
Gambhir's loyal fans also slammed the Indian board and a hashtag named #bringbackgambhir was soon trending on social micro-blogging site Twitter.
The BCCI had skipped the deadline for announcing the team and threatened a pull-out from the Champions Trophy over the dispute with the International Cricket Council (ICC).
India's Mohammed Shami celebrates dismissing South Africa's Quinton de Kock for seven runs during their Cricket World Cup match at the Melbourne Cricket Ground (MCG) February 22, 2015. But the decks have been cleared for India to defend the title they won in 2013.
The Indian squad will be picked on Monday, said a statement by Amitabh Choudhary, acting Honorary Secretary of the Board of Control for Cricket in India. Star all-rounder Yuvraj Singh, who made a successful comeback in the ODI side against England, has retained his place in the team along with Hardik Pandya. "That shows he is fit and not like others who are getting rehabilitated after surgery", Prasad said.More news: Russian President Vladimir Putin warns West to 'stop intimidating North Korea'
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India have belatedly named their Champions Trophy squad, nearly two weeks after missing the initial deadline.
Chaired by MSK Prasad, the committee has entrusted to Mahi's vast experience in the game. "We considered Rishabh Pant, Kuldeep Yadav, Suresh Raina, Dinesh Karthik, and Shardul Thakur who are in our standby list for Champions Trophy".
"We respect IPL but in the longer format, we have to also consider the English conditions that we are playing in".
"We don't have a great record against India in major events, but every day is a new day and I am sure the players will perform well in the first match". He had hurt his shoulder during the Test series against Australia and had conceded that recovering in time for the Champions Trophy was unlikely.
The playoffs start in England with India taking on Pakistan on June 4.