Use one few genes instead of reference genome in mapping

Hi.

My aim is to generate a phylogenetic tree from my analysis.

For this, I have a reference genome and Illumina reads of multiple samples.

I was thinking of using my own gene list generated from sequences downloaded from NCBI instead of using a reference genome for mapping.

Is this approach correct or do you guys have a simpler way?

Any suggestion will be much appreciated.

Thank you.