Xanthophyllomyces dendrorhous - Genome sequencing and assembly. Phaffia rhodozyma strain:CBS 6938

Xanthophyllomyces dendrorhous is a basidiomycete yeast that produces carotenoids, mainly astaxanthin. Astaxanthin has commercial interest due to its antioxidant and coloring properties. X. dendrorhous has a functional SREBP (Sterol Regulatory Element-Binding Protein) pathway being protein Sre1 the SREBP homolog in this yeast. The objective of this study was to identify the Sre1 direct target genes through high-throughput strategies, which included RNA-seq and ChIP-exo assays using as reference genome of X. dendrorhous the genome assembly that we report in this project. The genome was sequenced by single-molecule real-time (SMRT) sequencing using the Pacific Biosciences (PacBio) Sequel system and assembled by a hybrid assembly pipeline developed by Cold Spring Harbor Laboratory (Cold Spring Harbor, NY, USA) using the obtained PacBio reads and available reads of the same strain (CBS 6938) that were obtained by an Illumina HiSeq machine with 100 bp paired-end chemistry (PRJEB6925). The identified Sre1 direct target genes belong to the sterol and carotenoid biosynthesis pathways. These results demonstrate that Sre1 is a sterol master regulator conserved that also regulates the carotenogenesis in X. dendrorhous.