Background
Cultured pearls are unique gems produced by living organisms, mainly molluscs of the  Pinctada genus, through the biomineralization properties of pearl sac tissue.  Improvement of P. margaritifera pearl quality is one of the biggest challenges that  Polynesian research has faced to date. To achieve this goal, a better understanding of the  complex mechanisms related to nacre and pearl formation is essential and can now be  approached through the use of massive parallel sequencing technologies. The aim of this  study was to use RNA-seq to compare whole transcriptome expression of pearl sacs that  had producing pearls with high and low quality. For this purpose, a comprehensive  reference transcriptome of P. margaritifera was built based on multi-tissue sampling  (mantle, gonad, whole animal), including different living stages (juvenile, adults) and  phenotypes (colour morphotypes, sex).
Results
Strikingly, few genes were found to be up-regulated for high quality pearls (n = 16)  compared to the up-regulated genes in low quality pearls (n = 246). Biomineralization  genes up-regulated in low quality pearls were specific to prismatic and prism-nacre  layers. Alternative splicing was further identified in several key biomineralization genes  based on a recent P. margaritifera draft genome.
Conclusion
This study lifts the veil on the multi-level regulation of biomineralization genes 38 associated with pearl quality determination.