Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
BMC Genomics. 2020 Nov 26;21(1):834. doi: 10.1186/s12864-020-07244-z.
Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies.
Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine.
Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis.
黏红酵母被认为是一种具有生物技术重要性的产油红色酵母，可合成具有广泛工业用途的许多有价值的化合物。黏红酵母最显著的特性之一是形成充满类胡萝卜素的细胞内脂滴。然而，黏红酵母中这些有价值化合物生物合成的基本基因组特征尚未得到充分记录。为了揭示黏红酵母的生物技术潜力，我们通过下一代测序和基于 HPLC-MS 的代谢组学技术进行了基因组学和脂质组学分析。
在这里，我们首次将黏红酵母 ZHK 的基因组组装成 21.8Mb，包含 30 个 scaffolds 和 6774 个预测基因，N50 长度为 14、66、672bp，GC 含量为 67.8%。基因组完整性评估（BUSCO 比对：95.3%）表明基因组组装具有高质量的特征。根据基因组的功能注释，我们预测了几个涉及脂质和类胡萝卜素代谢以及某些工业酶生物合成的关键基因。比较基因组学结果表明，在五个黏红酵母物种中，大多数直系同源基因经历了强烈的纯化选择，特别是负责类胡萝卜素生物合成的基因。此外，我们还通过脂质组学方法鉴定了 982 种脂质，主要包括三酰基甘油、二酰基甘油三甲基高丝氨酸和磷脂酰乙醇胺。
通过全基因组鸟枪法测序，我们全面分析了黏红酵母的基因组，并预测了几个涉及脂质和类胡萝卜素代谢的关键基因。通过进行比较基因组学分析，我们表明在五个黏红酵母物种中，大多数直系同源基因经历了强烈的纯化选择。此外，我们还通过脂质组学方法鉴定了 982 种脂质。这些结果为进一步推进黏红酵母的生物技术应用提供了有价值的资源。
