Just as the 2D ellipse represents a 3D circle, the minor axis is extremely useful to us because of how that minor axis line coincides with and aligns with the normal vector - the 3D line that shoots straight off the surface of the 3D circle, completely perpendicular to that surface.
This means that we've got two ways of establishing the orientation of our circle in 3D space, as we draw it on our 2D page:
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The degree (width) of the ellipse controlling the circle's rotation
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The minor axis of the ellipse controlling the orientation of the circle's normal vector - basically the direction that the circle is facing.
If we need our circle to be oriented in a specific way in a more complicated scene, we will actually be able to start out with a normal vector line, then use it as the minor axis for our ellipse, drawing the ellipse around it so the line splits it into two equal, symmetrical halves, down its narrowest span.