Discovery of reads originating from the chloroplast with multiple congeners' reference

Question

[Plant_man_217]

I am trying to figure something out, but I might be over thinking it. I have some RADseq data for a non-model plant species and I would like to determine which, if any, of the reads might have originated from the chloroplast. There is no reference chloroplast genome for the species I am working with but five of its congeners have one. Can I just map reads to the chloroplast genome of the closest relative, or is there some way I can use all of the chloroplast genomes that are available?