Yellow thread is sort of a “standard” when sewing jeans and denim. Though I have seen garments with indigo thread used on most seams, with the heavy yellow thread used on certain “accent” areas of the garment.
I have sewn lots of denim (or heavy twills) and I like to use a contrasting thread at times. Just for fun. (On a pair of black jeans, I used fuscia thread, on a pair of indigo jeans, I used teal thread. Yeah, I’m a real rebel.) I don’t think people guess that these garments are hand-made. (They always seem surprised when I tell them.)
DuckDuckGoose is right about the crotch seam - reinforce that seam area a lot (A LOT) so it won’t bust out. Also, denim ravels like hell - finish your seams extra well. (I use a straight stitch and then serpentine stitch over each seam to finish.) Yes, yes, more information than you ever asked for. I just like to ramble about sewing!