The reshuffle saw Banerjee, West Bengal Chief Minister, rewarding her close associates with additional responsibilities and elevating former Union Minister Dinesh Trivedi to the vice-presidents' post and Roy was left in the cold.
"Trinamool Congress has appointed Subrata Bakshi, a party MP as additional all-India general secretary. He is a founder-member," party secretary-general Partha Chatterjee told reporters after the meeting.
Asked to explain the absence of Roy, a key party organiser, Chatterjee said "He (Roy) is busy with political activities and has been absent at the meeting by taking prior permission from the party".
Roy, a Rajya Sabha member who was recently quizzed by CBI in Saradha chit fund scam, being left out of additional responsibilities that were given to some of his party colleagues, came amid media speculation of differences between him and the party supremo.
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He also participated in the party's campaign for the by-election to Bongaon Lok Sabha and Krishnaganj Assembly seats in West Bengal which was held yesterday
Chatterjee said party MP Derek O'Brien, state Urban Development minister Firhad Hakim and party Lok Sabha member Kakoli Ghosh Dastidar were elevated to the national committee of the party.
He said O'Brien and the party Lok Sabha member Kalyan Banerjee would keep in touch with like-minded parties.
Mamata was reportedly upset about the absence of Roy in today's meeting.
Later, Roy told reporters replying to a question on the reason for his absence in the meeting that "Why I did not go, the party leader (Mamata Banerjee) knows. Anyway, whatever is done is done for the good.