"Trinamool's organisation will not be affected in any way by their exit," TMC secretary-general and education minister Partha Chatterjee told a press conference.
Thakur's son Subrata Thakur too joined the saffron party, which has hinted that many Trinamool Congress leaders were ready to switch over.
"If Manjul Krishna Thakur is so concerned about ideology and morality, why did he not resign as an MLA? Chatterjee said.
Earlier, Manjul told reporters, "I have decided to join the BJP today along with my son as I feel that the TMC is no longer a party for honest and good politicians. The TMC government has not allowed me to work for the benefit of my Matua community."
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The development came ahead of a crucial by-election to Bongaon parliamentary constituency in West Bengal on February 13.
TMC minister Upen Biswas, who was also present at the press conference, announced that Mamata Bala Thakur would be the TMC's candidate for Lok Sabha By-poll in Bongaon parliamentary constituency.