Differences in the lengths of the chloroplast genomes of two different strains of the same specie?

Hello,

I've been working on the assembly of a chloroplast genome from a microalgae. I did a reference assembly with a specific strain and I got 98% alignment with the reference sequence. I also did another assembly with another strain but I got 81%. So, my question is, what are the possible reasons for the differences between the genome architecture, even when they are from the same specie?
And I also need to add that there are more geographic proximity within the strain that I'm working and the strain that represented 81% alignment, more than the other strain with more coincidence.

Thanks in advance.