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SEATTLE — Amazon.com Inc. will acquire Whole Foods Market Inc. for $13.7 billion, including debt, in the biggest deal ever for the e-tailer as it continues to encroach on the grocery sector.

Amazon will pay $42 a share in cash for the natural food chain, the companies said today. Whole Foods cofounder and chief executive officer John Mackey will continue to run the business.

“Millions of people love Whole Foods Market because they offer the best natural and organic foods, and they make it fun to eat healthy,” Jeff Bezos, Amazon’s founder and CEO, said in a statement. “Whole Foods Market has been satisfying, delighting and nourishing customers for nearly four decades — they’re doing an amazing job, and we want that to continue.”

“This partnership presents an opportunity to maximize value for Whole Foods Market’s shareholders, while at the same time extending our mission and bringing the highest quality, experience, convenience and innovation to our customers,” said Mackey.

Whole Foods will retain its name and Austin headquarters. Completion of the deal, expected to close by year-end, is subject to approval by the company’s shareholders, regulatory approvals and other customary closing conditions.

Amazon’s biggest prior acquisition was three years ago, when it agreed to purchase video-game service Twitch Interactive Inc. for some $970 million in cash.

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