Influence of quality of genome assembly for RNA-seq read mapping

[Julien Roux]

Dear all,
I am wondering how much the quality of the reference genome assembly influences RNA-seq read mapping (for example Illumina reads mapped to the genome with Tophat). I could not find any published study addressing this question.

Do you know any paper where RNA-seq mapping rates and quality are compared between model species genomes, draft genomes and de novo assembled genomes?

Thanks!
Julien