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The Blues suffered a 1-0 defeat in the semi-final second leg, having held the holders to a goalless draw in the first leg, to exit the competition at the last four stage against the French outfit for the second successive season.
Despite the setback, Houghton declared she could not be more pleased with her side’s spirit, courage and togetherness.
“Over two legs, we gave everything,” she declared. “Again, defensively, we were superb – we just couldn’t manage to create a moment like they did.
“Fair play to Lucy for putting it in the back of the net She’s scored a few wonder goals and I was hoping she wouldn’t get one against us.
“I’m proud of the girls. We are a young, inexperienced team but we gave everything over two legs.
“This team has consistently grown. We play football in the right way and conduct ourselves in the right way.
“It’s important we keep progressing. It wasn’t meant to be but it wasn’t for the lack of effort or commitment.”
With City still in a strong position to retain the Women’s Super League title, Houghton urged her side to bounce back and use their disappointment as motivation for the remainder of the season.
“It’s important we focus. We have five big games left in the league and we still have another trophy to fight for.
“The league is in our hands and we have to make sure we recover as quick as we can.
“We play Bristol next (on Thursday) and we know that will be a tough one as well. It’s all about making sure we stay together like we did over these two legs and continue to fight for the next five games.”
Nick Cushing’s side suffered a 1-0 defeat to four-time winners Lyon at the Parc Olympique Lyonnais, courtesy of former Blue Lucy Bronze’s first-half volley.