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Preheat your oven to 350 degrees.
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Grease baking dish with butter or nonstick cooking spray.
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Cook pasta according to package instructions.
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Melt 2 tablespoons butter in a large skillet over medium heat.
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Chop your onion finely. Add to the pan and cook until tender, about 3-5 minutes.
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Reduce the heat to low and add the pumpkin puree, almond milk, cheddar cheese, ¼ cup of your Parmesan cheese, nutmeg, thyme, salt, and pepper to the skillet. Stir to combine ingredients until cheese is melted and the sauce is smooth.
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Add the drained penne and stir to evenly coat noodles in the sauce. Pour into baking dish. Melt remaining 1 tablespoon butter in a small bowl and add panko breadcrumbs.
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Stir to combine and sprinkle evenly over top of the penne. Bake uncovered for 20-25 minutes until heated through. Sprinkle with remaining ¼ cup Parmesan and chopped parsley before serving.
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Enjoy! :D