chloroplast genome does not map to reference

[hanz]

Hi,

I would like to ask,
I have assembled chloroplast genome of cultivated species using Getorganelle, and got circular.
However it does not mapped to reference (wild species) genome.
Is it something wrong with the genome assembly or any other insight?
Thank for help!

[Ben3]

hanz could you say a little more about what process you used to prep and sequence this chloroplast genome? Also, did you use any other tools?

[hanz]

Thanks for your reply.
I used chloroplast DNA and sequenced by Hiseq2000.
Sorry, do you mean others tools for alignment? I aligned using Geneious mapper.

[Ben3]

Sorry for the delay hanz. How old is the reference genome and where did you get it from? Also, is there any chance of contamination in your samples? This is always the biggest issue that I have had with assemblies in the past.