Transcriptomic and metabonomic analyses reveal roles of VPS 29 in carotenoid accumulation in adductor muscles of QN Orange scallops

In our previous studies, we demonstrated that the accumulation of carotenoids in QN Orange scallops might be regulated by the vacuolar protein sorting 29 (VPS29) gene. VPS genes are involved in pigments accumulation (including carotenoids) in some species and VPS29 is known as the core component of the membrane transport complex Retromer. However, the possible mechanism of carotenoids accumulation underlying the VPS29 remains unexplored. This study aimed to further elucidate the roles of VPS29 in the carotenoid deposition. Transcriptomic analyses revealed four differentially expressed genes related to carotenoid accumulation, including three down-regulated genes, low-density lipoprotein receptor domain class, scavenger receptor, Niemann Pick C1-like 1, and one up-regulated gene, ATP binding cassette transporter in RNAi group. Results from metabonomic analyses indicated increased profiles of retinol and decreased fatty acids between the RNAi and the control group. It thus speculated that VPS may be related to the accumulation of carotenoids as RNAi of VPS 29 seemed to result in a reduction in pectenolone through the blockage in the absorption of carotenoids and an accelerated cleavage of carotenoids into retinol. •The vacuolar protein sorting 29 gene may have modulated pectenolone accumulation.•Differentially expressed genes and metabonomic related to carotenoid pathway were analyzed between RNAi and control groups.•VPS 29 RNAi seemed to induce pectenolone reduction by decreasing carotenoid absorption and accelerating carotenoid cleavage.