Genomic and metabolomic insights into the biosynthesis of carotenoids and lipids in oleaginous red yeast Cystofilobasidium infirmominiatum HZR20 isolated from Mangrove plants in Southern China

Cystofilobasidium infirmominiatum, biotechnologically significant yeast, is increasingly garnering attention due to its superior ability to produce valuable carotenoids and lipids. Nonetheless, until now, the reference genome that governs the biosynthesis of carotenoids and lipids in C. infirmominiatum remains unreported. Here, the first genome assembly of C. infirmominiatum was performed through integrating Oxford Nanopore and Illumina NovaSeq techniques. The assembled genome is 27.61 Mb in size, comprising 35 scaffolds, with a N50 length of 1,144,974 bp and a GC content of 68.21%. It was predicted to encompass 10,719 protein-coding genes, with functional annotation conducted on 8,045 utilizing the NR database. Moreover, C. infirmominiatum was capable of synthesizing at least 3 carotenoids, 839 Lipids, 1,876 volatile organic compounds, and 540 other metabolites, as revealed by LC/GC-MS-based metabolomic profiling. Integrative multi-omics analysis identified key carotenogenic and lipogenic genes, as well as their related metabolic intermediates. The findings presented herein significantly improve our comprehension of the biosynthetic mechanisms of carotenoids and lipids in C. infirmominiatum. It furnishes a valuable genomic and metabolomic framework that facilitates fundamental molecular biology and comparative genomics studies, thereby broadening our insights into the genetic features and evolutionary dynamics of this species.