An Apple supplier that has partnered with the company on a sapphire glass plant in Arizona filed for bankruptcy protection on Monday after its sapphire crystal wasn't used for iPhone 6 and 6 Plus screens.

GT Advanced Technology's glass is expected to be used in two of the three versions of Apple Watch and it is continuing to operate. However, the company's stock price has fallen more than 95% over the past month.

The company's stock was trading at $0.80 Monday afternoon. It had been trading at almost $20 in July largely on the expectation that GT's glass would be used in the iPhone 6.

Apple and GT announced plans to build a component manufacturing facility in Mesa, Arizona, last November. Apple pledged to provide GT with a prepayment of about $578 million, which GT would pay back over a five-year period, starting in 2015.

Though Apple used sapphire crystal for the fingerprint sensors in its iPhone 5S, the company declined to say which Apple products would use sapphire glass made by GT. When Apple announced its two new iPhone 6 models in September, some fans were disappointed upon learning they sported Gorilla Glass rather than sapphire crystal, as had been rumored. On the Mohs scale of mineral hardness, sapphire crystal rates a 9 out of 10, versus 6.8 for Gorilla Glass 3. (Diamond rates a 10.)

It's not clear why Apple opted not to use sapphire crystal for the screens of the iPhone 6 and 6 Plus. Neil Alford, a minerals expert and professor at Imperial College, told Mashable that Apple may not have been confident that GT could produce sapphire crystal on a large scale.

Though the apparent snub has wreaked havoc on GT's fortunes in the short term, Tom Gutierrez, president and chief executive officer of GT, touted the company's "strong and fundamentally sound underlying business," in a written statement.

"Today's filing does not mean we are going out of business," he added. "Rather, it provides us with the opportunity to continue to execute our business plan on a stronger footing, maintain operations of our diversified business, and improve our balance sheet."

UPDATE: Oct. 7, 1:16 pm EST On Tuesday, GT's shares had recovered and were trading for as much as $1.63.