Wonnacott has been a key figure in Torquay Under-18s domestic treble success this term.
And his progress has seen him make the first team's bench towards the end of the campaign.
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“Unfortunately after offering Matt Wonnacott a two-year pro deal, he and his family have decided for him to sign a professional deal with Wigan,” United boss Gary Johnson told the club's official website.
“We wish him well, albeit disappointed about his decision.
"I’d like to thank Chris Todd and Kenny Griffiths, along with our senior goalkeepers Mark and Shaun, for their work that they’ve done with Matty over the last couple of seasons.”
Head of Youth Todd added: “It does show we are doing something right, if Championship clubs sign our youth players.
"We’ve put all our efforts in trying to make him better, and we feel we’ve done that.
"It shows the quality of the coaching and the education that players are getting and proves that we are doing a good job within the club.
"That’s due to all the staff involved, so it’s a big pat on the back to them really.
“It’s a shame that he’s not signed with Torquay, because that was the pathway, but he is going to a Championship club, and we do wish him well with that.”